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  1. Mar 2024
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    1. 27. Water clarity: Which of the following best describes your ability to see the stream bottom?Low water clarity is typically seen as a cloudy or dark appearance to the water.This may be due to particles in the water, depth, or water color.Select one.o 1. Very clearo 2. Mostly clearo 3. Slightlyo 4. Not clear at allVery Clear Mostly Clear Slightly Clear Not clear at allCan perfectly seestream bedCan see more than 2 feetinto the waterCan see 6 inches to 2 feetinto the waterCan see less than 6 inchesinto the water28. Color: Which color best describes the color of the water?Please select the color of the water as it appears in front of you.Select one.o No apparent color (Clear)o Blueo Greeno Yellowo Browno Blacko Other, please describe: _______________________End Group: Water ColumnGroup: Stream BedIn this section, please focus on the stream bed, which is the bottom of the stream.For each question, please select the description that best matches the conditions of the stream bed.29. Aquatic Plants: Which of the following best describes the amount of aquatic plants in thestream?Aquatic plants grow from the bottom of the stream or on the surface of the waterThis does not include algae or plants that are growing on the stream bank.Select one.o 1. Noneo 2. Minimalo 3. Moderateo 4. Dense

      Questions that may be hard to understand provided detailed explanation or charts to show that the question entails.

    2. Stream Bank Vegetation: Which of the following best describes the plant growth on the streambank or directly adjacent to the stream?Select one.o 1. Noneo 2. Minimalo 3. Moderateo 4. Dense24. Pipes: Can you see any pipes going into or near the stream from your current position.Please only report what you can see in from your current position, you do not need to move up ordownstream to answer this question.Select one.o Yes → Continue to #25o No → Skip to #27o Cannot tell → Skip to #2725. How many pipes can you see?Select one. If you select “3 or more”, please upload a photo at the end under “Important Feature”.o 1 → Skip to #27o 2 → Continue to #26o 3 or more → Continue to #2626. Please identify the approximate size of each pipe you can seeWrite the number of pipes that the following sizesSmall (less than 1 ft diameter): _______________Medium (1 to 5 ft diameter): _________________Large (greater than 5 ft diameter): ____________

      Content question continue: Questions are short with super short responses. Short responses doesn't allow the reader to overcomplicate the answer.

    3. Location descriptionPlease describe the sampling location. (i.e. road name, access directions – sampled from bridge or trail tostream, etc.)________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________13. What is the name of the stream?Please write the name of the stream you are performing this survey about.Write “DK” if you do not know.________________________________________________________14. Are you currently on public land or private land?Public land refers to state, county, or town parks, public fishing rights easements, boat launches. Fishingplatforms and other public recreational areasPrivate land refers to property owned by an individual, company, or organization that is not intended forpublic recreationo Public lando Private lando Do not know15. Where are you positioned in relation to the stream while performing this survey?Select one.o Wading in streamo On stream bank (less than 3 feet from water edge)o 3 – 10 feet from water edgeo Bridge or pier overlooking streamo Paddling in stream (in canoe, kayak, etc.)o On motorized boato Other, please describe: _____________________________16. What are the current weather conditions?Select one. If you select other, please describe.o Sunnyo Partly cloudyo Cloudyo Raino Other (snow, hail, etc.), please describe: ______________________________

      These are also background questions! These questions are more related to the content and therefore ease the reader into the harder content questions. These questions ask simple things about the information of location and background information that might explain or alter their results.

    4. Which of the following best describes your knowledge of water quality?Please select the description that best matches your knowledge of water quality prior to performing thissurvey.Select one.Likert style:o 1. No knowledgeo 2. Somewhat knowledgeableo 3. Very knowledgeableo 4. Extremely knowledgeable9. What was your primary reason for coming to the stream today?Select one. If you select other, please describe.o Hikingo Swimmingo Wadingo Fishingo Motor-boatingo Paddling (canoe, kayak, etc.)o To perform surveyo Other, please describe -10. What do you plan to do at the stream today?Select all that apply. If you select other, please describe. Perform survey Hiking Wading Swimming Fishing Motor-boating Paddling (canoe, kayak, etc.) Wildlife viewing Other, please describe: ____________

      These are the background questions! They are easy to answer and simple questions that are leading into the content questions. These questions make the reader more comfortable and confident when moving to next section.

    1. La lectura Pensar o no pensar, éste es el rating presenta la disminución del lenguaje y la capacidad de pensar en la actualidad, el uso de la televisión y artículos tecnológicos han disminuido el hábito de la lectura y nos están limitando a imaginar y crear nuestras propias imágenes mentales a partir de la lectura. Por ende esta lectura nos invita a recuperar la importancia de la lectura como una herramienta fundamental para la criticidad, creatividad y la construcción de una sociedad reflexiva y enérgica.

    2. Es preciso recordar que la humanidad siempre ha requerido de la comunicación a través de la palabra, para estructurar en ideas los conocimientos y la experiencia adquirida a través del tiempo, que le ha permitido evolucionar. Una de las destrezas que ha desarrollado el pensamiento es la lectura, al principio con la tradición oral y luego cuando aparece la escritura; pero hoy, ya no leen, sino que observan imágenes de hechos que no analizan. Si el ser humano se queda con las palabras sin significación porque no realiza el acto de leer, la posibilidad de seguir desarrollándose sería mínima o nula. Lamentablemente como se menciona en el documento, el ciudadano ha empezado desde mediados del siglo pasado, con la invención de herramientas como la televisión, de dispositivos electrónicos, el deterioro de su capacidad de comprender que para transformar el mundo y lograr la interacción social, hay que desarrollar su pensamiento. Por consiguiente, al no practicar las habilidades comunicativas se está convirtiendo en un zombi o títere, una persona sin pensamiento. En estas condiciones, con pensamiento vacío, sin imaginación dominarán su voluntad y no tomarán decisiones propias, incluso pueden ir en contra de sí mismos. Esto constituye un peligro para una sociedad que no va a defender sus derechos ni de los demás. Creo que el mundo necesita buscar un punto de equilibrio, en donde todos podamos vivir en armonía, sin destruir a nuestros hermanos. Entonces, considero que hoy deberíamos tomar en cuenta la pedagogía de la liberación que nos propone Paulo Freire para combatir poco a poco la idea de despojarnos del pensamiento.

    3. La pérdida del balance en el uso de las nuevas tecnologías lleva a coartar la capacidad de generación de las propias ideas; capacidad que se desplaza y reemplaza la motivación de opinar y crear por algo que al parecer ya está hecho, que esta imaginado o dicho con la tendencia de volvernos simplemente espectadores de los acontecimientos. El estudio en Harvard demuestra que estamos ante una involución que ha sido más notoria en la última década; esta castración de la tecnología “esconde” intereses comerciales y desvaloriza lo realmente importante, el desarrollo continúo de nuestras capacidades, que creo es el verdadero propósito del avance tecnológico.

    4. En la actualidad la humanidad nos hemos convertido en consumidores compulsivos de la tecnología ya que no solo en la televisión encontramos ilustraciones imaginadas y creadas por otros, actualmente encontramos gran contenido visual en redes sociales, y como lo menciona el autor "quedarnos sin palabras es quedarnos sin pensar" y es tan cierto esto, en muchos de los casos solo repetimos patrones que vemos en las pantallas e inclusive con palabras que muchas veces no tienen sentido creamos historias que nuestra ignorancia trata de comprender y por esa misma razón no estamos en la capacidad de corregir al otro.

      La lectura con un libro físico en mano actualmente ya no se mira, lo que sostenemos en mano es un teléfono y podemos decir "LEYENDO" pero lo que se lee son contenido o comentarios de farándula y sin contenido enriquecedor; todo esto provoca que las personas cada vez carezcan de un buen vocabulario y que su pensamiento sea menos critico, esto nos hace un llamado a concientizar para empezar auto educarnos, dedicarnos un tiempo para enriquecer nuestro vocablo y nuestros pensamientos.

      Los docentes estamos llamados a incentivar, motivar y ser mediadores e ir formando en nuestros estudiantes el habito de la lectura para que en un futuro su manera de expresarse sea con pensamientos bien fundamentados y críticos.

    5. Las personas cada vez están quedándose sin palabras y sin pensamiento. Esto sucede por el consumo excesivo de lo que se ve a través de una pantalla. Miran y aceptan toda la información que aparece en las redes sociales. ¿Cuántas horas al día pasamos pegados a nuestros celulares? Seguramente más horas de las que se dedica a la lectura de un libro o a la conversación con la familia. Esa pantalla no potencia la palabra, por el contrario, mantiene a los individuos callados e hipnotizados. Por eso, muchas veces se ha visto en los restaurantes o espacios públicos como los adultos dejan en las manos de los infantes un celular que los mantiene con los ojos abiertos como planos y en completo silencio. Ante esta situación resulta necesario mencionar que alguien que lee va a desarrollar la imaginación, el pensamiento crítico, la creatividad y otras capacidades. Todos los que vemos a la lectura como el camino del cambio deberíamos incentivar a los demás a tomar un libro y descubrir nuevos mundos, perspectivas y palabras.

    6. (Pensar o no Pensar, éste es el rating) escrito por Ramiro Diez es un excelente texto que está dirigido a un público globalizado y habla acerca de cómo la televisión afecta nuestra vida ofreciendo estereotipos que la gente se impulsa a seguir de manera negativa. El autor hace uso de argumentos muy sólidos que sustentan su punto de vista y llevan al lector a la reflexión acerca de lo que estamos observando día a día en diferentes medios televisivos y tecnológicos donde gran parte de la información que se difunde está pensada en un tinte comercial misma que resulta perjudicial, porque en muchos casos la verdad es vacía de contenido.

    1. si se concibe a la lectura y a la escritura como prácticas sociales, suaprendizaje debe estar lo más apegado posible a la realidad circundantede quien aprende. Al respecto, Virginia Zavala (2008) expresa que la literacidadestá presente en la mente humana, en los textos leídos o escritos y sobre todo semanifiesta a nivel social.

      Las macrodestrezas lingüísticas son concebidas como prácticas sociales. Resulta imprescindible aprender a hablar y escuchar para comunicarse de manera oral. También, saber escribir todo lo que se quiere expresar. A su vez, poder leer cualquier tipo de texto. Todos estos aprendizajes deben estar relacionados con el contexto del que está aprendiendo. Por eso, los materiales para trabajar la asignatura de Lengua y Literatura deben ser textos propios del entorno. Por ejemplo, leer noticias locales o dialogar sobre acontecimientos relevantes del barrio o institución educativa.

    2. Bloque 2. Comunicación ora

      El perfeccionamiento en habilidades de comunicación oral es fundamental en los distintos niveles de educación, permite al estudiante un adecuado desenvolvimiento social, afectivo de escucha y razonamiento de lo percibido por el sentido auditivo, y a la vez poder emitir posturas razonadas complementadas por la expresividad corporal, permite en su conjunto una forma de comunicación asertiva. El desarrollo de está destrezas permiten adecuarse a los distintos ambientes sociales, académicos que en virtud de los niveles reviste de complejidad progresiva, la socialización y la expresividad son el vehículo más que contribuye al aprendizaje. En el caso particular, el permitirse tiempos durante la clase para explorar aspectos personales de cada estudiante (dependiendo del número de estos en clase) en donde con un nivel menor de formalidad (conversación, charla, opiniones sobre distintos temas) se puede establecer un clima de confianza; estas formas de expresiones. son tan importantes cómo los contendidos académicos y permite identificar situaciones personales que afecten el desempeño individual. En un ámbito más formal la asignación de temas específicos relacionados con la materia impartida, interviniendo a manera de moderador, explicando la importancia de cada temática expuesta, muchas veces lo que empieza cómo una exposición de un grupo termina siendo un conversatorio o debate con la intervención de algunos o de la mayoría de los estudiantes, lo cual establece también un clima de confianza. El aporte del docente a través de experiencias es importante a la vez motiva al estudiante a expresarse.

    3. a enseñanza de la lengua y de la literatura debe acompañarse de la disponibilidadque tiene que ver con la presencia física de objetos (libros, periódicos, revistas, en-ciclopedias, afiches, CD-Rom, entre otros) que puedan ser leídos o que sirvan paraproducir escritos. Así, esta propuesta curricular incorpora las bibliotecas de aulacomo un elemento importante para el aprendizaje

      hay que tener en cuenta que la lengua y literatura es una materia muy importante en la formación de un estudiante ya que de esta depende de como el estudiante se desenvuelva en el futuro, claramente menciona aqui que es indispensable incorporar las bibliotecas de aula como un elemnto importante para el aprendizaje, y si bien es cierto si un estudiante lee mucho tiene un plus en la manera de captar las cosas ya que su mente esta abierta

    4. Escritura creativa

      La escritura creativa permite que los estudiantes exploren en sus cabecitas para crear y generar textos en base a sus experiencias sueños o actividades cotidianas.

      Para abordar este tema es importante realizarlo como juego, para que no sea tan aburridor este espacio, para ello podemos usar el juego de palabras para crear una historia . Otra actividad que podemos utilizar es "La bolsa con cosas" en la que podemos colocar diferentes elementos y los estudiantes realicen una historia que salga de su imaginación tomando como herramienta de inspiración el elemento que saque de la bolsa.

    5. Más importante que estudiar de-finiciones formales o desmontar los elementos de una estructura literaria, es eldespertar en el estudiante el hábito y el placer por la lectura.

      De a cuerdo a la Literatura en contexto nos indica que debemos incentivar a los estudiantes para generar en ellos el habito y placer por la lectura mas no aburrirlos con el estudio de las funciones o elementos de la escritura literaria, para ello es necesario que los estudiantes tomen la literatura como un recurso para la imaginación, la creación de pensamientos simbólicos.

      Para abordar este bloque podemos usar textos que despierten el interés de los estudiantes, en este caso con la ayuda de bibliotecas virtuales podemos encontrar textos relacionados con historia mundial, textos ecuatorianos y otros; tomando como herramienta diccionarios virtuales para investigar el significado de las palabras nuevas que se vayan encontrando en la lectura, y así desarrollar la comprensión lectora.

    6. Usar la lengua oral exige un dominio de las destrezas de escucha y de habla queen la mayoría de situaciones se producen de manera simultánea. Por esta razón, sepensó unificarlas en el bloque denominado “Comunicación oral”, en vez de plantearun desarrollo por separado de la escucha y del habla, con la finalidad de que setrabajen de manera conjunta en situaciones comunicativas concretas.

      La comunicación oral es muy importante porque exige el dominio del escuchar y el hablar, desarrolla en los estudiantes el lenguaje oral y no se lo considere de forma alterna ya que es fundamental, la interacción entre el lenguaje oral y el escrito es permanente. Es importante tomar en cuenta que el lenguaje de interacción social permite que los estudiantes tengan criticidad de valor. La expresión oral permite la narrativa que describa y argumente ante una audiencia, por otra parte, el expresar y comprender le permiten manejar formas de comunicación. Los estudiantes al ascender de subnivel la capacidad de lenguaje se perfecciona, es por eso muy importante que contribuyamos con bases sólidas a esta macrodestreza. “JUEGO DEL VEO VEO”.- consiste en describir objetos del entorno el que acierte inicia el juego nuevamente. CONTAR LA HISTORIA.- Consiste en iniciar contando una historia sobre cierto tema de interés de los estudiantes y seguido cada uno le aumenta algo a la historia, sumado lo que anteriormente se dijo. El REY MANDA O SIMON DICE.- consiste en que una persona dice que le traigan un objeto y seguido de eso quien lo encuentra lo va describiendo. JUEGO DEL DRAMA.- consiste en que uno de los niños escoge un personaje e inventa un drama. CREANDO RIMAS.- consiste en crear rimas de agrado de los estudiantes y luego exponerlas en clase. COMPARTO MI HISTORIA.- consiste en formar grupos en el aula y permitirles que escojan un tema sobre el que pueden conversar y al final sacar una reflexión.

    7. Por otro lado, estos conocimientos y capacidades se potencian y fortalecen, gra-cias a la mediación del docente, quien ayuda a los estudiantes a construir significa-dos y a atribuir sentido a lo que aprenden. La clave del aprendizaje de la lenguaescrita reside en el grado de significatividad y sentido que los estudiantes otorgana la lectura y a la escritura y al propio acto de aprenderlas

      Los docentes somos los llamados a ser mediadores al momento de enseñar la lengua, todos los estudiantes no aprenden de la misma manera ni traen los mismo conocimientos o concepciones de lo que normalmente se enseña en la escuela es por eso que los maestros estamos en la obligación de proporcionar las herramientas necesarias para que los estudiantes al momento de practicar la lengua escrita puedan construir significados y así generar sentido a lo que aprenden al leer y escribir.

    8. Además, esta propuesta curricular aporta al desarrollo del pensamiento lógico, crí-tico y creativo, al estimular la inteligencia lingüística que involucra el aprendizaje delas macrodestrezas, como herramientas indispensables del razonamiento verbal, elenriquecimiento del vocabulario de los estudiantes y de su capacidad para esta-blecer relaciones lógicas de diverso tipo entre nociones y conceptos. También, lacomprensión de textos contribuye al desarrollo de destrezas de pensamiento comola inferencia, el análisis y la síntesis

      La enseñanza de Lengua y Literatura nos permite como docentes aportar al correcto desarrollo del pensamiento en los estudiantes, nos permite interactuar con los chicos a través de la lectura, además con los correctos ejercicios aplicados en el momento de leer, les ayudamos a mejorar su vocabulario, que a futuro les permitirá expresarse de una manera correcta y generar ideas o conceptos críticos y creativos

    9. La enseñanza de la lengua y de la literatura debe acompañarse de la disponibilidadque tiene que ver con la presencia física de objetos (libros, periódicos, revistas, en-ciclopedias, afiches, CD-Rom, entre otros) que puedan ser leídos o que sirvan paraproducir escritos. Así, esta propuesta curricular incorpora las bibliotecas de aulacomo un elemento importante para el aprendizaje

      Este apartado detalla la importancia del Lenguaje como aprendizaje en las y los estudiantes considerando fundamental y primordial en el desarrollo de las destrezas, sin duda alguna se debe de tomar en cuenta los diferentes niveles de adquisición del aprendizaje de cada uno de los estudiantes sin dejar a un lado las necesidades y los recursos didácticos que se empleen en cada clase.

    10. La enseñanza de la lengua y de la literatura debe acompañarse de la disponibilidadque tiene que ver con la presencia física de objetos (libros, periódicos, revistas, en-ciclopedias, afiches, CD-Rom, entre otros) que puedan ser leídos o que sirvan paraproducir escritos. Así, esta propuesta curricular incorpora las bibliotecas de aulacomo un elemento importante para el aprendizaje.

      Considerando que el presente currículo toma como base la disponibilidad física de objetos, menciona libros, revistas, periódicos, entre otros que sirvan para producir escritos por medio de la incoporación de bibliotecas de aula como elemento importante para el aprendizaje. ¿Qué estrategias toma el estado para enriquecer las bibliotecas escolares en instituciones educativas si tomamos en cuenta que "Actualmente el número de bibliotecas escolares es ínfimo: de 12.184 instituciones educativas fiscales, solo 679 tienen una biblioteca escolar, es decir, solo el 5,7%". fuente: Diario La Hora.

    11. Otra consideración importante sobre cómo los estudiantes aprenden, desarrollan yse apropian de la lengua oral y escrita la refiere Vygotsky (1979). Hace más de 60años, este psicólogo soviético definió la importancia de la relación y la interaccióncon otras personas, como origen e inicio de los procesos de aprendizaje

      Tomando esta cita como resultado de un estudio psicologico verídico, puedo entender la importancia de la socialización en la vida del estudiante, ha de considerarse las relaciones de éste como fuente de los conceptos que aprende, razón por la cual el trabajo del docente es afectado por el entorno del estudiante pudiendo ser un detonador de dificultades en el aprendizaje del alumno, o en su defecto un potenciador de habilidades según las personas que participen en su aprendizaje fuera de la escuela.

    12. comunicación oral, lectura y escrituraaborda destrezas específicas que integran el uso de las Tecnologías de la Informa-ción y la Comunicación (TIC) para apoyar y mejorar las capacidades de expresiónoral y escrita e incentivar la curiosidad intelectual, promoviendo el trabajo autóno-mo y organizado.Por último, la labor que se desarrolla en torno a la lengua, entendida como cultura,y a sus expresiones literarias contribuye de manera significativa a que los estu-diantes se aproximen, de manera reflexiva e indagadora, a la realidad socioculturaldel país para comprenderla mejor y fortalecer el sentido de identidad. De estamanera, se incentiva a los estudiantes a indagar y a tomar conciencia de la lenguaescrita como vehículo de producción, transmisión y conservación de la cultura, y acomprender que la diversidad lingüística es la base de una sociedad interculturaly plurinacional, concebida en un marco de interacción respetuosa.Contribución del área de Lengua y Literaturaal perfil de salida del Bachillerato ecuatoriano2

      El uso de las TIC contribuyen al proceso de enseñanza- aprendizaje en los estudiantes, ya que brinda oportunidades para acceder a un mayor conocimiento, habilidades o destrezas. A diferencia de los estudiantes que estudian en un campo rural, que tienen menor posibilidad de acceso a la tecnología. Recordando que para el uso de un dispositivo electrónico se necesita la concientización por parte de los estudiante y que puedan sacar provecho de esta herramienta que es muy útil en la vida cotidiana.

    13. Al tomar en cuenta el carácter social de la lengua, el enfoque constructivista recono-ce que los estudiantes no son todos iguales. No todos tienen los conocimientos ni lascapacidades que la escuela enseña. Por lo tanto, los procesos de enseñanza debendiferenciarse según la cercanía o distancia con respecto a la “cultura escolar”.

      Considero que este párrafo aborda un tema social importante como la igualdad, considera abiertamente que las capacidades y conocimientos diferencian a unos de otros entre los estudiantes, creo en la importancia de esta afirmación en razón de que permite tomar acción para sortear estas diferencias con un enfoque constructivista aplicando un proceso de enseñanza o didáctica que sea acorde a la cercania o distancia con relación a la "cultura escolar".

    14. Clima de aula afectivo. El clima afectivo y emocional de las relaciones en el aulaes fundamental para lograr la participación y, por ende, el aprendizaje de los estu-diantes. Por otro lado, en función de la lectura y escritura, el clima de aula debeenfrentar a los estudiantes a los actos y objetos de la cultura escrita. Emilia Fe-rreiro (1999) dice acertadamente que si se desea que el niño empiece a construirconocimiento sobre la lengua escrita, esta tiene que estar presente en sus entornos.Considerando esta necesidad, el aula debe transformarse en un ambiente alfabeti-zador que permita el acercamiento de los estudiantes, de manera espontánea,a diferentes tipos de texto (libros, revistas, folletos, carteles) que contribuyan adar sentido al manejo competente de la lengua y de la literatura. Los intercambiosque se realicen en el aula deben promover la problematización, la curiosidad yel interés sobre múltiples y diferentes temas que motiven y guíen su satisfacciónmediante el uso de la lengua oral y/o escrita

      Sin duda el docente juega un papel fundamental en el aprendizaje, el clima afectivo y emocional en las relaciones del aula es indispensable para promover la participación de los estudiantes en la construcción de los aprendizajes, en este sentido se puede inducir de forma espontanea la exploración de diferentes tipos de textos que contribuyan al uso competente de la lengua y literatura.

    15. Con respecto a la enseñanza de la Literatura, los textos literarios son abordados enun proceso gradual, desde cuatro perspectivas: 1) como disfrute y placer en juegosde palabras, adivinanzas, amorfinos, trabalenguas, etc.; 2) como representación dela cultura o culturas y motivo de actitud estética; 3) como diferentes formas de lamanifestación humana, y 4) como testimonio en los cuales se reconocen tenden-cias o movimientos históricos. Este diálogo está dentro de un enfoque crítico y, portanto, de una posición crítica, en razón de que considera el arte literario como unproceso que interviene en la formación de una actitud crítica frente al mundo

      La actitud crítica del estudiante se debe ir incentivando de manera gradual, como primer paso debería ser el crear una necesidad real para el aprendizaje, luego implementar algunas herramientas pedagógicas e ir avanzando a prueba y error todas esas perspectivas que aborda la literatura, nunca olvidar como el entorno de cada estudiante puede influir en la eficacia de usar estas herramientas, ya que al final también se debe evaluar los resultados que obtengamos.

    Annotators

    1. o simplify, jamming causes the receiver to die, spoofing causes the receiver to lie.

      This is an expert summation and simplification. The author has taken two complicated types of attacks that can appear similar to each other, and differentiated their symptoms in order to create a single sentence that provides all necessary information in the form of a rhyme.

    1. La mayoría de los pacientes se presenta con disnea, fatiga o ambas, en tanto que el edema, dolor torácico, presíncope y síncope son menos frecuentes y se relacionan con la enfermedad más avanzada. En las fases tempranas de la PAH, la exploración física a menudo resulta normal. Conforme la enfermedad progresa, puede haber evidencia de insuficiencia ventricular derecha con elevación de la presión venosa yugular, edema de extremidades inferiores y ascitis.

      Sintomas

    1. The preliminary survey received 561 enrollments. Over the course ofthe experiment, 121 cat-owner pairs completed Trial 1 (~22 % of total);53 completed Trial 2 (~9% of total); 43 completed Trial 3 (~8% oftotal); 38 completed Trial 4 (~7% of total); 34 completed Trial 5 (~6%of total); and 30 completed Trial 6 (5% of total). Of the 30 thatcompleted the experiment, the nine subjects that made at least onestimulus selection came to 16 total stimulus selections: the square waschosen on eight occasions; the Kanizsa was chosen o

      The result was a bit confusing for me to understand? How did this work out?

    1. es necesario aclarar que la educación no se reduce a la institución -escolar o familiar-, pues independientemente de su existencia, educar es la espontaneidad de lo humano en lo humano, el bien que poseemos para seguir adelante. Es por esto que educar siempre es un movimiento hacia adelante pues busca acoger y acompañar con el único fin de que podamos permanecer como especi

      La educación va más allá de las instituciones formales. Es importante reconocer que el aprendizaje se da en todas las facetas de la vida. Esto significa que no solo adquirimos conocimientos en el aula o en casa, sino que también aprendemos de nuestras interacciones cotidianas, de nuestras experiencias y de nuestro entorno social y cultural. Asimismo, se resalta que la educación capacita al ser humano para progresar tanto a nivel personal como colectivo. Este proceso de crecimiento y desarrollo es constante, permitiéndonos evolucionar como individuos y contribuir al avance de la sociedad.

    2. La pregunta de cómo llevar al plano del método dichos conceptos es la gran cuestión del pedagogo pero también su creatividad. Por ejemplo, María Montessori y los «rincones de creatividad del niño» muestran la actualización de dichos conceptos pues el paso de un rincón al otro y de una actividad a otra significa la puesta en escena de la libertad y la conveniente modificación de su naturaleza a través de la experiencia de diversas sensaciones.

      En el campo educativo es importante recalcar grandes precursores de la educación como Maria Montessori, una reconocida y valorada psicopedagoga que siempre se preocupó por el bienestar de los niños,es más siempre comparó que los niños son como una esponja porque todo lo que escuchan o miran siempre van absorber.Por lo tanto una de sus estrategias como parte de la didáctica fue la creatividad,misma que le permitió impulsar que los niños puedan ser libres, aprender de diversas sensaciones y a la vez puedan fomentar su autonomía y aprendizaje.

    3. La educación, actividad propiamente humana, plantea de tiempo atrás lagran cuestión sobre la naturaleza y la libertad del hombre. Tanto naturalezacomo libertad son conceptos extremadamente complejos aunque en susdiversas acepciones conservan, el primero, la condición de cambio y, elsegundo, el de autodeterminación. Por naturaleza entendemos aquí laesencia del ser y su movimiento, lo que es propio al ser en cuanto no es otracosa, por ejemplo, arte o fabricación. El principio esencial de la naturalezaes su movimiento y esto significa que potencialmente puede devenir otro ensu misma especie. En su materialidad, un árbol es un árbol y una roca es unaroca, su materia se conserva y su movimiento la transforma. La naturaleza,por el movimiento, conserva la potencia del cambio y mantiene su cualidad.La cualidad del árbol es ser madera y la de la roca devenir piedra o arena.

      En este párrafo nos invita a realizar una profunda reflexión sobre la naturaleza humana y la libertad en relación con la educación. La educación como actividad humana se presenta como un espacio donde se manifiestan tanto la naturaleza como la libertad humana.

      La naturaleza se entiende como la esencia del ser y su movimiento, que está en armonía con el ser y no. Así, la naturaleza preserva el poder del cambio y preserva su calidad.

      Por otro lado, la libertad se presenta como el derecho a la autodeterminación, un concepto que también es complejo y multifacético. En el contexto de la educación, la libertad puede interpretarse como la capacidad de un individuo de dirigir su propio aprendizaje y desarrollo.

      El texto nos invita a pensar sobre la educación como actividad humana ya que esta se encuentra en una encrucijada, también nos invita a pensar cómo la educación puede promover el desarrollo de la naturaleza y la libertad personal

    4. Digamos, entonces, que la pedagogía es la reflexión sobre el acto de educar. O mejor aún, "la pedagogía es una reflexión sobre los fines de la educación y sobre los medios que uno puede poner al servicio de dichos fines" (Meirieu, 1997: 231). Esta definición, esta idea de pedagogía, reconoce el poder del método -sensualista, naturalista, objetivista, etc.- y al hacerlo crea las diferentes vertientes de la pedagogía.

      La pedagogía es el estudio de la educación y del proceso de enseñanza-aprendizaje. Se enfoca en cómo se transmiten los conocimientos, las habilidades los valores y las normas de una generación a otra. Ésta ciencia abarca un amplio espectro de conocimientos y enfoques que tienen como objetivo mejorar los procesos educativos y contribuir al desarrollo integral de las personas.

    5. La educación nueva es activa por naturaleza pues ve en el niño su capacidad de educación, aprendizaje y el despertar de sus dones. Cada niño, cada niña, conserva en su naturaleza la potencialidad de su movimiento, de su libertad. A partir de aquí la pedagogía recubrirá un conjunto de expresiones todas novedosas respecto de la pedagogía tradicional o la del Viejo Régimen.

      Se contrasta la pedagogía tradicional en la cual el docente era el centro del proceso educativo con la nueva educación, en donde se propone estrategias y metodos que se ajustan a las necesidades de cada niño, convirtiendolo en el principal agente de su aprendizaje, reconociendo sus capacidades, potencial y talentos, además, convierte al docente en un guía del eprendizaje para el desarrollo integral de las nuevas y futuras generaciones.

    1. Task Generalization. To generalize to new NLG tasks,Meta NLG tasks follow the same modality as the target task.For example, if our target task is to adapt to DA-utterancepairs in a new domain, then DA-utterance pairs in each Tiare sampled from the same source domain. We also consideradapting to new DA types in later experiments. In this case,DA-utterance pairs in each Ti have the same DA type. Thissetting merges the goal of task generalization.

      Tổng quát hóa bài toán: Để có thể tổng quát hóa các bài toán NLG mới, các bài toán Meta NLG sẽ đi theo phương thức giống với các bái toán mục tiêu. Ví dụ, nếu bài toán mục tiêu là thích ứng với các cặp DA-utterance ở trong 1 miền mới, thì các cặp DA-utterance ở mỗi Ti sẽ được lấy mẫu từ cùng miền gốc.

    2. the idea of our Meta-NLG algorithm isto repeatedly simulate auxiliary Meta NLG tasks from Ds tomimic the fine-tuning process in Eq.(2).

      Ý tưởng chính của thuật toán Meta-NLG là lặp lại việc mô phỏng các bài toán Meta NLG từ tập dữ liệu Ds để bắt chước quá trình fine-tuning ở biểu thức (2).

    1. Creating a vision board is a great way to display thoughts and goals especially leading into your career. It shows what qualities and traits are needed to achieve career aspirations, and it can even portray people or ideas that have helped pave your path. The vision board below displays my goal of becoming an I/O Psychologist to help organize and increase employee productivity in the workplace.

      good intro. Eases the reader into your story.

    1. O thou invisible spirit of wine, ifthou hast no name to be known by, let us call theedevil!

      Iago forced the drinks on him, and therefore he is the "devil" and yet, Iago has done nothing but let normal events carry out, because the devil is in Cassio himself, and in everyone. Does the wine signifying Jesus's blood mean anything for this?

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    1. N
      1. Máquina passa por processo de aprendizagem, na análises de imagens de câncer de seio
      2. Na sequência, imagens são revisadas por ela com a finalidade de identificar tumores
      3. A máquina se demonstra mais acurada no reconhecimento dos tumores do que os médicos
      4. Há uma expectativa de que a máquina substitua um dos médicos que, em dupla, avaliam atualmente os exames no sistema de saúde pública do Reino unido, reduzindo pela metade a mão de obra utilizada no processo.
      5. Segundo pesquisadores que acompanham o experimento, a máquina poderá também diminuir a fadiga dos médicos que fazem laudos a partir de exames de image.
    1. secuencia de oraciones carece de tema global o macroestructura, el conjunto es percibido como una sucesión de enunciados incoherentes, y, por lo tanto, no llega a constituirse como texto.

      La macroestructura textual es el contenido semántico global que representa el sentido de un texto y se refiere a la estructura semántica del conjunto del texto. Junto con la superestructura textual, que se refiere a la forma en que se organiza la información y forma la estructura global del texto en sí. La macroestructura es importante para la coherencia y permite que el texto se perciba como una unidad de comunicación.

    2. La macroestructura textual es la idea principal o el tema central de un texto. Es lo que le da coherencia y sentido global. Sin una macroestructura clara, el texto puede parecer confuso. Este concepto ayuda a entender cómo se organizan y se comprenden los textos.

    3. La macroestructura textual se encuentra confirmada por diversas partes, y cada una de ellas cumple con un rol importante, ya sea en un cuento, leyenda, artículo científico, entre otras ya que cada una de ellas desarrolla partes fundamentales para que el lector pueda llegar a obtener una buena comprensión de lo que está leyendo. Si la lectura no estuviera compuesta por la macroestructura se vuelve un texto incoherente que el lector no va a entender debido a que no se está cumpliendo con sus estructuras normas o leyes de escritura para que sean entendidas de una manera correcta y se concrete el mensaje que cualquier lectura quiera dejar al lector.

    4. La macroestructura textual es muy importante para la comprensión y para darle coherencia a un determinado texto, tomando en cuenta la semántica, la idea principal y la organización de ideas para emitir un mensaje claro o conocer que nos quiere transmitir sin abordar tanto contenido.

    1. Um estudo publicado em abril de 2023 pelo Instituto Igarapé informa que no ano de 2018 o crime ambiental se tornou a terceira atividade criminosa mais lucrativa do mundo, ficando atrás apenas do tráfico de drogas e do contrabando. [2]

      Fonte: Conjur, 03/2024

      Lucratividade da atividade criminosa (U$D 110 a 281 bi) 1. Tráfico de drogas 2. Contrabando 3. Crimes ambientais

      Lavagem de dinheiro da atividade criminosa com

      1. Pecuária irregular
      2. Extração de madeira
      3. Mineração ilegal

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    1. Me parece importante que lxs científicxs consideren estas herramientas para ser más eficiente el labor científico. Sin embargo creo que se debería realizar herramientas, como metadatos, curación de datos y accesibilidad para gente no científica. Tener algunos repositorios por ejemplo de contenido de divulgación para que la gente no especializada pueda informarse y como viene en la figura 2, se manejen los datos a nivel nacional o incluso mundial.

    1. S
      1. O lucro per capta por trabalhador sexual forçado é de £21,000 / ano
      2. A exploração sexual é de longe é a atividade mais lucrativa no trabalho forçado.
      3. Os trabalhadores sexuais forçados correspondem a 27% do total e geral 73% dos lucros do "negócio"
      4. Lucro com trabalho forçado alcança $236bn e alcança 27 milhões de pessoas.
    1. "
      1. Sistemas alimentares são responsáveis por 30% das emissões de gases de efeito estufa
      2. Produtos de origem anila respondem por quase 60% destas emissões
      3. Pecuária gera 14% de todas as emissões de carbono, produzido números semelhantes aos de todos os transportes juntos.
      4. Com expansão das pastagens há perda de biodiversidade e extinção de espécies silvestres.
      5. A atividade pecuária usa intensivamente água
    1. Wyniki Cho były mniej widoczne w tym badaniu.Obserwowano tendencję do obniżania stężenia choliny w prążkowiu.Dzieci otrzymujące Cho (1,25 g. Dwuwinian Cho w proszku dostarczającyCho) miał wyższą inteligencję niewerbalną, wyższe umiejętności wzrokowo-przestrzenne, wyższą zdolność pamięci roboczej, lepszą pamięć werbalną i mniej objawów behawioralnych ADHD niż osoby otrzymujące placebo.Niski poziom Cho może wynikać z nieprawidłowego metabolizmu Cho.Stosunek Cho/kreatyna zmniejszył się o 12% w prawej korze przedczołowej po leczeniu stymulantem.Analiza regionalnego mózgu wykazała znacznie zmniejszony sygnał związków zawierających Cho po leczeniu MPH.Metabolity Cho nie wykazały żadnych zmian w odpowiedzi na leki.U dzieci z ADHD obustronny stosunek Cho/Cr prążkowia wykazywał łagodny jednostronny wzrost. Wydaje się, że występuje łagodna nadpobudliwość układu cholinergicznego.

      Cholina a metylofenidat i struktury mózgowe

    2. Cholina jest niezbędnym mikroelementem, uznanym przez Stany Zjednoczone (USA) Instytut Medycyny w 1998 roku [49]. Mechanistycznie jest prekursorem neuroprzekaźnika mózgowego acetylocholiny i fosfolipidów błonowych, w tym fosfatydylocholiny [50,51]. Jest to również donor metylu, o którym wiadomo, że odgrywa kluczową rolę we wzroście i rozwoju mózgu, utrzymując funkcjonalną i strukturalną integralność błony komórkowej [36]. Poprzez działanie metabolitów bierze udział w szlakach zaangażowanych w metylację genów związanych z pamięcią i funkcjami poznawczymi [36].Jak pokazano w Tabeli 1, w kilku badaniach mechanistycznych zbadano wpływ i mechanizmy choliny na rozwój mózgu. Wiadomo, że płód i noworodek mają wysokie zapotrzebowanie na cholinę, a rola mikroelementu w metylacji DHA i histonów jest uważana za modyfikator genów zaangażowanych w aspekty uczenia się i pamięci [52].Bekdash i in. (2016) opisują, w jaki sposób cholina jest ważnym epigenetycznym modyfikatorem genomu (zmieniającym metylację genów, ekspresję i funkcję komórki), przy czym nieprawidłowe poziomy podczas rozwoju płodowego i/lub wczesnego życia po urodzeniu są powiązane ze zmienionymi funkcjami pamięci w późniejszym dorosłym życiu [53]. Cholina jest również potrzebna do prawidłowego rozwoju pamięci, prawdopodobnie ze względu na zmiany w rozwoju ośrodka pamięci (hipokampa) w mózgu [54]. Uważa się, że cholina wpływa na proliferację komórek macierzystych i apoptozę, a tym samym potencjalnie modyfikuje strukturę i funkcję mózgu [55].Modele mysie pokazują, że poporodowe leczenie choliną może modulować plastyczność neuronów, zapobiegając deficytom w koordynacji ruchowej, jednocześnie zwiększając gęstość kolców dendrytycznych i morfologię neuronów [56]. Stwierdzono ponadto, że cholina częściowo przywraca dendrytyczną złożoność strukturalną w mysich neuronach hipokampa, które mają niedobór żelaza [57]. Inne prace pokazują, że zmniejszone zapasy choliny podczas ciąży mogą utrudniać i zmniejszać liczbę progenitorowych komórek mózgowych kory mózgowej (NPC), przy czym dotyczy to dwóch typów NPC – promieniowych komórek glejowych i pośrednich komórek progenitorowych, co wskazuje, że dostawy choliny regulują rozwój kory mózgowej [58]. Mysi model skupiający się na autyzmie wykazał, że suplementacja choliny podawana potomstwu matek z niedoborem reduktazy metylenotetrahydrofolianu (MTHFR) miała potencjał do osłabienia fenotypu autystycznego [59].Dalsze badania wykazały, że suplementacja choliny poprawia upośledzenie interakcji społecznych w mysim modelu autyzmu, pomagając zmniejszyć deficyty w zachowaniach społecznych i zmniejszyć lęk [60].

      Prenetalny poziom choliny wpływa na rozwój zdolności motorycznych, pamięci, hipokampa,

    3. Wcześniejsze prace sugerowały, że cholina nie wydaje się być wrażliwa na leczenie metylofenidatem u dzieci [83]. Jednak analiza regionalnych widm mózgu w 2008 r. wykazała znacznie zmniejszony sygnał związków zawierających cholinę po leczeniu metylofenidatem [84]. Uważa się, że jest to zgodne z najnowszą hipotezą energetyczną ADHD - że niewystarczająca podaż mleczanu do oligodendrocytów prowadzi do upośledzenia syntezy kwasów tłuszczowych i tworzenia osłonki mielinowej, co może odpowiadać za obniżony poziom choliny [84,85].Według Wiguna i in. (2012) leczenie stymulantem (długo działającym metylofenidatem) przez 12 tygodni wydaje się indukować zmiany neurochemiczne (uważa się, że odzwierciedlają poprawę neuroplastyczności) w korze przedczołowej u dzieci [86]. W szczególności stosunek choliny do kreatyny zmniejszył się istotnie u dzieci (średnia wieku 8,5 roku) o 12,4% w prawej korze przedczołowej i o 16% w lewej korze przedczołowej [86]. Było to badanie pilotażowe, więc konieczne jest powtórzenie badań.

      Mniejsze stężenie choliny u osób stosujących metylofenidat w porównaniu z tymi, którzy ni estosowali

    4. Koncentrując się na badaniach obrazowych, Alger i in. (2021) zastosowali obrazowanie tensora dyfuzji całego mózgu [78]. Wyniki pokazały, że dzieci z ADHD (w wieku 8–13 lat) narażone na "prenatalna ekspozycja na alkohol" (PAE) miała cięższą patologię istoty białej w porównaniu z osobami bez PAE [78]. Wśród osób z ADHD + PAE wyniki Tower Test Achievement (wyższe dla lepszej wydajności) korelowały ujemnie z choliną, przy czym jej rola była nieco niejasna i wymagała dalszych badań [78]. Dodatkowe prace neuroobrazowe mierzące istotę białą przedczołową wykazały, że poziom choliny w przedniej koronie promienistej był o 27% niższy u dzieci i młodzieży z ADHD + PAE w porównaniu z osobami z idiopatycznym ADHD [79]. Inne badania rezonansu magnetycznego wykazały, że20–25% neuronów mogło umrzeć lub być poważnie dysfunkcyjnych u pacjentów pediatrycznych z ADHD i wydawało się, że występuje łagodna nadaktywność układu cholinergicznego (układu, który obejmuje syntezę i wydzielanie acetylocholiny) [80].

      Wpływ choliny na mózg w ADHD

    5. Uważa się, że stan odżywienia (w tym niski poziom choliny) odgrywa kluczową rolę w nasileniu i częstości występowania podstawowych objawów ASD [67]. Badania na ludziach koncentrowały się na potencjalnej roli choliny w odniesieniu do ASD (Tabela 2).Po pierwsze, prace z wykorzystaniem obrazowania spektroskopowego u dzieci z ASD (w wieku 3–4 lat) wykazały, że poziom choliny w istocie szarej i białej był obniżony w porównaniu z dziećmi normalnie rozwiniętymi [68,69]. Koncentrując się na składzie istoty białej, inne prace wykazały również, że ASD i jego nasilenie były związane z niższym poziomem choliny w istocie białej mózgu, wraz z korą okołosylwijską [70]. Podobnie Margari i in. (2018)stwierdzono, że poziomy metabolitów mózgu (stosunek choliny/Cr) są znacząco zmienione w istocie białej płata czołowego u osób z ASD w porównaniu z grupą kontrolną [71]. Hardan i wsp. (2008) zaobserwowali niższy poziom choliny po lewej stronie wzgórza u dzieci z autyzmem [72]. Niektóre badania wykazały, że niższy poziom choliny we wzgórzu jest skorelowany z wynikami behawioralnymi u dzieci z ASD (7–18 lat), tj. zwiększonym nasileniem stereotypowych zachowań i upośledzeniem komunikacji [73].Jeśli chodzi o charakterystykę metaboliczną, Wang i in. (2022) przebadali 29 chłopców z ASD i 30 typowo rozwijających się chłopców (średni wiek ≈ 3 lat) [74]. Chłopcy z ASD mieli niższy poziom choliny w osoczu, co było niekorzystnie skorelowane z wynikami ABC języka.ustalenia, które są zgodne z Gabis i in. (2019) [74,75]. Rzeczywiście, praca Wanga i wsp.(2022) stwierdzono również, że produkty pośrednie metabolizmu choliny, takie jak fosfatydylocholina i lizofosfatydylocholina (zaangażowane w metabolizm glicerofosfolipidów), były zmniejszone, co sugeruje, że może to mieć wpływ na procesy metabolizmu choliny i późniejsze upośledzenie zdolności językowych u dzieci z ASD [74]. Dodatkowe prace dotyczyły efektów suplementacji. Gabis i in. (2019) przeprowadzili randomizowane badanie z podwójnie ślepą próbą, w którym oceniano łączne działanie donepezylu i choliny (350 mg/dobę przez 8 tygodni w fazie badania otwartego) w porównaniu z placebo [75].Grupa leczona miała trwały wpływ na receptywne umiejętności językowe u dzieci z ASD przez 6 miesięcy po leczeniu, przy czym bardziej znaczące efekty zaobserwowano u dzieci w wieku poniżej10 lat [75].Inne badania opisują nawykowe spożycie choliny i stan. Naukowcy korzystający z danych z badania U.S Autism Intervention Research Network for Physical Health (AIR-P) stwierdzili, że 60-93% dzieci z ASD spożywało mniej niż zalecane odpowiednie spożycie choliny [76]. Dzieci z autyzmem miały również niższy poziom choliny w osoczu niż zdrowe grupy kontrolne [76]. Autorzy doszli do wniosku, że spożycie choliny było niewystarczające u znacznej liczby dzieci z ASD, co może przyczyniać się do nieprawidłowości w metabolizmie jednego węgla zależnym od kwasu foliowego obserwowanym u wielu dzieci z autyzmem [76]. Bardzo podobne wyniki podali Hyman i in. (2012) [77]. Analiza 3-dniowej dokumentacji żywieniowej dzieci z ASD w wieku 2–11 lat wykazała, że niewiele osób z ASD lub dopasowanych osób z grupy kontrolnej spełniało zalecane poziomy spożycia choryny [77].

      Wpływ braku choliny na powstanie ASD i jego objawy, suplementacja cholin

    1. De acordo com o Ministério da Saúde, o Brasil registrou até a última 6ª feira (15/3) 1.684.781 casos de dengue desde o começo de 2024. Esse número supera o total de casos registrados ao longo do ano passado inteiro. O ano de 2024 já é o 2º pior da série histórica, atrás apenas de 2015, quando o país contabilizou mais de 1,688 milhão de casos de dengue. No entanto, com mais de nove meses pela frente até o final do ano, é quase certo que 2024 se confirmará como o pior da série histórica da doença no país.

      Estatísticas 1. Casos de dengue de 2024 já superam o ano de 2023. 2. A pior marca da série histórica, 2015, deve ser batida em 2024.

    1. A 500 nm10 mV 15.3 log ph/s/cm210 secB> 30 - ~- 400E 30 460-- o/50020 -*- 520'N 20 ! ~ ,o570/10. /3 - 600? !13 14 15 16Log Irradiance(photons/s/cm2)C-253 -e- cell 62-4) -3 -o -A- all cellsnomogram-4400 500 600Wavelength(nm)Fig. 2. Spectral tuning of light response inphotosensitive ganglion cells. (A) Voltage re-sponses of a single cell to a 500-nm narrow-band stimulus at indicated intensities (in log1ophotons s-1 cm-2). Baseline - -60 mV foreach trace. (B) Plots of peak depolarization as afunction of log retinal irradiance for each ofseveral narrow-band spectral lights (400- to600-nm wavelength, as indicated; 10-nm widthat half height); same cell as in (A). Peak wasobtained from a 1-s boxcar average of rawvoltages. (C) Spectral sensitivity functions de-rived for photosensitive ganglion cells from rel-ative displacements of intensity-response func-tions along the abscissa in (B). Red curve: samecell as in (A) and (B). Green curve: group datafor all cells (n = 34; number of cells tested perwavelength as follows: 400 nm, 5; 420 nm, 3;440 nm, 2; 460 nm, 4; 480 nm, 4; 500 nm, 34;520 nm, 7; 540 nm, 5; 570 nm, 2; and 600 nm,2). Black curve: nomogram for retinal -basedphotopigment with kmaxof 484 nm (411, fit byleast squares method to the group data.www.sciencemag.org SCIENCE VOL295 8 FEBRUARY2002 1071This content downloaded from 137.22.14.85 on Fri, 17 Apr 2015 19:40:35 UTCAll use subject to JSTOR Terms and Conditions

      These graphs are very descriptive. Having the highs and lows of. the voltage stimulation is very good to see.

    Annotators

    1. år du opfordrer eleverne til at reflektere over deres oplevelse med at skrive ogdele deres tekster, kan du guide dem med konkrete spørgsmål og anbefalinger, der kan hjælpedem med at formulere deres tanker og følelser på en meningsfuld måde. Her er nogle ideer til,hvad du kan bede dem om at overveje:1. Spørgsmål om skriveprocessen:o Hvordan følte du dig, mens du skrev din erindringsskildring?o Hvilke udfordringer stødte du på undervejs, og hvordan håndterede du dem?o Hvilke tanker og følelser forsøgte du at udtrykke gennem din tekst, oghvordan forsøgte du at formidle dem?2. Refleksion over brugen af sproglige billeder:o Hvordan brugte du sproglige billeder og stilistiske elementer til at skabestemning og udtrykke dine følelser og oplevelser?o Var der bestemte sproglige billeder eller passager, der var særligtbetydningsfulde for dig, og hvorfor?3. Evaluering af den kreative proces:o Hvordan føler du, at din erindringsskildring blev modtaget af klassen?o Hvordan føler du, at du voksede som forfatter eller fortæller gennem denneskriveøvelse?o Er der noget, du ville gøre anderledes, hvis du skulle skrive dinerindringsskildring igen?4. Diskussion af læringsoplevelsen:o Hvad har du lært om d
    2. det er en klog tilgang for at imødekomme forskellige niveauer af elevernesforståelse og færdigheder. Her er en tilpasset version af undervisningsforløbet, der inkludererlette og svære opgaver:Lektion 1: Introduktion til "Barndommens gade" og besjæling (45 minutter)1. Præsentation af digtet og dets temaer (15 minutter)o Introducer Tove Ditlevsens digt "Barndommens gade" og dens temaer,herunder tab, barndom og længsel.o Fokuser på digtets følelsesmæssige dybde og symbolske betydning.2. Besjæling: Definition og eksempler (30 minutter)o Forklar begrebet besjæling og dets betydning i litteraturen.o Identificer eksempler på besjæling i digtet og diskuter deres funktion ogvirkning.Lette opgaver:o Eleverne kan identificere og diskutere konkrete eksempler på besjæling idigtet med støtte fra læreren.Svære opgaver:o Eleverne kan identificere og analysere hvordan besjæling bruges til atudtrykke digtets temaer og stemning på egen hånd.Lektion 2: Analyse af besjæling og andre sproglige virkemidler (45 minutter)1. Gennemgang af sproglige virkemidler (25 minutter)o Gennemgå forskellige sproglige virkemidler såsom besjæling, metaforer,personifikation og symbolik.o Diskuter hvordan disse virkemidler bruges til at skabe stemning og udtrykkedigtets temaer.Lette opgaver:o Eleverne kan identificere og forklare forskellige sproglige virkemidler medstøtte fra læreren.Svære opgaver:
    3. Her er undervisningsplanen med perspektivering til Edgar Allan Poe's "TheRaven":Lektion 1: Introduktion til "Barndommens gade" og besjæling (45 minutter)1. Præsentation af digtet og dets temaer (15 minutter)o Introducer Tove Ditlevsens digt "Barndommens gade" og dens temaer,herunder tab, barndom og længsel.o Fokuser på digtets følelsesmæssige dybde og symbolske betydning.2. Besjæling: Definition og eksempler (30 minutter)o Forklar begrebet besjæling og dets betydning i litteraturen.o Identificer eksempler på besjæling i digtet og diskuter deres funktion ogvirkning.Lektion 2: Analyse af besjæling og andre sproglige virkemidler (45 minutter)1. Gennemgang af sproglige virkemidler (25 minutter)o Gennemgå forskellige sproglige virkemidler såsom besjæling, metaforer,personifikation og symbolik.o Diskuter hvordan disse virkemidler bruges til at skabe stemning og udtrykkedigtets temaer.2. Analyse af besjæling i "Barndommens gade" (20 minutter)o Dyk ned i digtet og identificer passager, hvor besjæling bruges.o Diskuter hvordan disse besjælede objekter bidrager til digtets betydning ogfortolkning.

    Tags

    Annotators

    1. Además de volver a la prioridad de los grupos y de poner el énfasis en la gestión de grupo, también sugerimos otras características técnicas para esta concepción de red social colectiva: La red existe principalmente como comunicación social dirigida, destinada a un proyecto, y para que esto sea posible se le deberían añadir los diferentes foros de lenguaje naturales tales como debates y wikis. Sin embargo, a diferencia de las redes sociales tradicionales, el propósito del sitio web para redes sociales será ayudar a los usuarios a guardar y perfeccionar los datos, y los datos se guardarán en un formato abierto como RDF. Los usuarios y grupos tienen autorización para gestionar los datos del proyecto y para recuperarlos utilizando el marcado y la búsqueda. El mapeo se debería utilizar como un medio, posible y fácil de interpretar, para comprender la recogida colectiva de datos. Para los proyectos colectivos se podrá permitir el anonimato bajo determinadas condiciones (por ejemplo el grupo es totalmente anónimo, o el grupo decide abrirse al anonimato). Por ejemplo, en Ni Channel, una de las razonas por las que el inventor quiere que sea anónimo es para que no haya una segregación que podría perjudicar la formación de colectivos.[13] Solo el colectivo debería poder acceder a los datos personales, y ni siquiera quienes administran el servidor deberían poder acceder a ellos. En cuanto a la seguridad de las redes, en primer lugar los datos en los servidores se encriptarán mediante la implementación de infraestructuras de claves públicas, y el grupo se definirá por las claves públicas compartidas. Por tanto ni el ISP ni los administradores del sistema podrán acceder a los datos en el servidor. En segundo lugar, los datos se guardarán distribuidos en múltiples servidores a fin de minimizar las consecuencias de los ataques.

      Consejos de [[Yuk Hui]] sobre características que puedan tener redes sociales más colectivas.

    1. Chairman e CEO.

      O chairman é o presidente do conselho administrativo. Assim, na hierarquia organizacional, ele está acima do CEO. Neste caso, enquanto o CEO trabalha com o foco em desenvolver os objetivos do negócio, o chairman representa os interesses dos investidores e acionistas.

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

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      Summary:

      Henkels et al. propose the role of myotubularin-related proteins in promoting KRAS4B localization to the plasma membrane. Their data shows that shRNA-mediated knockdown of myotubularin-related proteins -2, -3, -4, or -7 led to measurable changes in RAS localization and in plasma membrane (PM) content. More specifically, knockdown of any one of these MTMR proteins led to a decrease in PI4P levels in the PM, an increase in PI3P content in the PM, a decrease in phosphatidyl serine (PtdSer) in the PM/whole cell, and a decrease in mutant KRAS localization to the PM. Their data also shows a decreased presence of ORP5 at the PM, a protein which is responsible for the exchange of PI4P in the plasma membrane for PtdSer in the endoplasmic reticulum. These results are somewhat predictable and are supported by the existing literature, as MTMR proteins are known to exhibit 3-phosphotase activity towards PI3P to generate PI (a precursor to PI4P), PI4P is known to recruit ORP5, and ORP5 is known to contribute to PtdSer content in the membrane [1, 2]. Regardless, the authors find that the individual knockdown of MTMR proteins is sufficient to cause measurable changes in PM content and mislocalization of mutant KRAS4B. Thus, despite the fact that many proteins are involved in regulating PM content, such as PI4KA, PtdSer synthase 1 and 2, Nir2/3, and PITPs, Henkels et al. speculate that MTMR proteins are the primary regulators of PtdSer PM levels [3, 4, 5, 6]. The authors propose that the loss of function in any one of these MTMR proteins alone is sufficient to cause significant changes in PM content through an ORP5-dependent process, and that this ultimately leads to a decrease in mutant KRAS signaling.

      Major comments:

      The unbiased siRNA screen used to identify proteins that impact KRAS membrane localization was a very nice approach to identify MTMR proteins. Although there is a clear phenotype of KRAS mislocalization associated with knockdown of the various MTMR proteins, the data provided does not prove a causational role for the MTMR proteins in maintaining PtdSer content, nor KRAS localization, at the PM. The current data does not provide a mechanism by which MTMR proteins are influencing this process, but rather speculates using existing literature that it is the loss in MTMR 3-phosphotase activity that leads to decreased PtdSer in the membrane. There is a series of conversions and exchanges that act upon PI3P (the substrate of MTMR proteins) and PI to generate PtdSer in the PM; thus, it is a dynamic process that is influenced by a variety of different proteins and transporters [3, 4, 5, 6]. To prove their single-protein-driven hypothesis, the authors should clone and express a mutant MTMR protein construct that contains an inactive phosphatase catalytic domain, to prove that it is indeed MTMR's generation of PI (which is further converted into PI4P) in the membrane that is responsible for maintaining PtdSer content and KRAS localization. Without this, there is not enough evidence to support this claim. In addition, the authors speculate that ORP5 is a critical intermediate in this process, and that the loss in PI4P/ORP5 at the PM following MTMR knockdown is responsible for the decrease in PtdSer at the PM. The authors should knockdown ORP5 in MTMR-wildtype cells, since it is downstream of their proposed mechanism, and see whether this leads to comparable reductions in PtdSer levels and KRAS mislocalization at the PM. This would confirm ORP5 as having a major role in this setting and would support the initial mechanistic hypothesis. These experiments are imperative to forming an appropriate conclusion, especially since some of their current data contradicts their mechanistic hypothesis: the authors identify a decrease in whole cell PtdSer content, not just PM PtdSer content, when MTMR proteins are knocked down. Based on this result, one would predict that a secondary or supporting mechanism must exist that contributes to a reduction in whole cell PtdSer content, which likely contributes to its loss at the PM as well. The authors describe in line 360 how "previous work has shown that PM PI4P depletion indirectly blocks PtdSer synthase 1 and 2 activities," to explain this reduction in total cell levels of PtdSer. The authors should look at PtdSer synthase 1 and 2 activities in the presence of MTMR knockdown, as the loss in PtdSer at the PM may rely more heavily on synthase activity than ORP-dependent transfer of PtdSer. Although the c. Elegans model that was used to investigate downstream let-60 (RAS ortholog) activity through a multi-vulva phenotype is quite intriguing, it is more critical to assess downstream RAS pathway activation, especially in the human colorectal adenocarcinoma or the human mammary gland ductal carcinoma cell lines. Not only would this line of questioning provide a higher significance and increase the clinical applicability of these findings, but it is also crucial to support the author's claim that MTMR knockdown can influence mutant KRAS activity. Although small changes in KRAS localization to the PM can have significant effects on downstream signaling, these effects need to be measured and confirmed in this setting. The authors should perform western blots to assess the activation of both the PI3K and MAPK pathway in the MTMR knockdown cell lines. In addition to this, it might be important to know whether there are any changes in the levels of the KRAS protein itself, as recycling/transport pathways may be impacted by its lack of recruitment to the plasma membrane. Finally, the authors show that proliferation is inhibited by MTMR knockdown as a readout of RAS activity. The authors should also assess the levels of cell death, as the inhibition of mutant KRAS in cancer cells would likely lead to cell death. The authors do not describe why reducing any one of the MTMR proteins alone is sufficient to deplete the PM of PtdSer. This sort of discussion is important for understanding compensatory or regulatory mechanisms in place between the MTMR proteins, as this may influence PtdSer levels at the PM. For example, it has been shown that MTMR2 can stabilize MTMR13 on membranes. Do the levels, stability, or localization of the other MTMR proteins change when one specific MTMR is knocked down? Is this why we see an effect on PtdSer in any one of the knockdowns? The authors should at the very least provide western blots for each of the MTMR proteins discussed in the presence of each individual MTMR knockdown.<br /> In addition to the above experiments, the MTMR hairpins should be expressed in a secondary or tertiary cell line to prove that these events are not specific to the current model used. Since their current human mammary gland ductal carcinoma cell line overexpresses a mutant KRAS-GFP construct, perhaps doing similar experiments in a cancer cell line that already expresses an endogenous mutant KRAS might provide a better model. Although this protein would not include a GFP-tag, other ways of visualizing its localization at the PM (such as immunofluorescent staining) could be used to confirm its localization there. In addition, the effects on downstream RAS signaling could be measured through western blot of PI3K and MAPK pathways. Supplemental Figure 4 is incorrectly referred to in the text as Supplemental Figure 3 (line 257-258). The text reads, "Confocal microscopy further demonstrates that HRASG12V cellular localization is not disrupted after silencing MTMR 2/3/4/7 (Fig. S3)" but Figure S3 is an EM image of PM basal sheets from T47D cells expressing GFP-KRASG12V. Supplemental Figure 4 shows that mutant HRAS is unaffected by the various MTMR knockdowns. Since the authors show decreased proliferation in mutant KRAS cells following MTMR knockdown, the authors should also investigate any changes to proliferation rates in mutant HRAS cell lines following MTMR knockdown. This data is necessary to prove that MTMR-driven changes in downstream RAS signaling are specific to mutant KRAS and not mutant HRAS. It may also be important for the authors to also show any effects on wildtype RAS localization to the PM when MTMR-2,-3,-4, and -7 are knocked down, to show whether this is a oncoprotein-specific event. <br /> The representative images chosen for Figure 4 diminish the reliability of the data, as it is difficult to see a visible change in the PI3P probe between the control and MTMR knockdown cells in these images. Since the authors rely on the Mander's coefficient and the number of gold particles throughout much of the paper, having the same conclusion quantitatively but not qualitatively for these assays is confusing. Perhaps the authors should elaborate on whether MTMR knockdown has a stronger effect on PtSer and KRAS PM presence than PI3P PM presence. They should also describe their method for identifying early endosomes, since they switch back and forth between describing the content of the PM and of early endosomes, such as in Figure 1 and Figure 4.

      Minor comments:

      An additional experiment that may add another layer of clinical applicability would be the use of an MTMR inhibitor in this cell line, to see whether similar effects can be achieved pharmacologically [7]. This would provoke other researchers to investigate MTMR inhibitors in vitro and in vivo to assess the effect on mutant KRAS cancers.

      The inclusion of cell lines that express KRAS proteins of different mutational statuses would be extremely interesting, as KRAS' orientation within the plasma membrane has been shown to be altered by these mutations. This fact should potentially be considered when choosing a secondary or tertiary cell line to do additional experiments in, but it is not necessary for the authors to elaborate on how MTMR proteins may impact different KRAS mutants for the scope of this project.

      The results of this paper rely heavily on one experimental technique, which is calculating a Mander's coefficient and counting the co-localization of the probe of interest with the CellMask stain of the plasma membrane. How this coefficient is derived is explained in appropriate detail in the methods section of this manuscript; however, a secondary route of identifying these changes in membrane constituents would greatly enhance the paper's conclusions. This would eliminate any doubt surrounding the accuracy of the technique, since so much of the data relies on one experimental output.

      References

      1. Clague MJ, Lorenzo O. The myotubularin family of lipid phosphatases. Traffic. (12):1063-9 (2005).
      2. Chung J, Torta F, Masai K, Lucast L, Czapla H, Tanner LB, Narayanaswamy P, Wenk MR, Nakatsu F, De Camilli P. PI4P/phosphatidylserine countertransport at ORP5- and ORP8-mediated ER-plasma membrane contacts. Science. 349(6246):428-32 (2015).
      3. Kim YJ, Guzman-Hernandez ML, Wisniewski E, Balla T. Phosphatidylinositol-Phosphatidic Acid Exchange by Nir2 at ER-PM Contact Sites Maintains Phosphoinositide Signaling Competence. Dev Cell 33: 549-561 (2015).
      4. Balla A, Balla T. Phosphatidylinositol 4-kinases: Old enzymes with emerging functions. Trends Cell Biol 16, 351-361 (2006).
      5. Arikketh D, Nelson R, Vance JE. Defining the importance of phosphatidylserine synthase-1 (PSS1): unexpected viability of PSS1-deficient mice. J Biol Chem. 283(19):12888-97 (2008).
      6. Cockcroft S. The diverse functions of phosphatidylinositol transfer proteins. Curr Top Microbiol Immunol. 362:185-208 (2012).
      7. Taylor GS, Maehama T, Dixon JE. Myotubularin, a protein tyrosine phosphatase mutated in myotubular myopathy, dephosphorylates the lipid second messenger, phosphatidylinositol 3-phosphate. Proc Natl Acad Sci U S A. 1;97(16):8910-5 (2000).

      Significance

      The significance of this paper lies in providing the field with an additional regulator of KRAS localization at the PM, as this is localization is critical to KRAS function. Despite three decades worth of understanding and even successfully blocking KRAS membrane localization in vitro, no KRAS-membrane-localization inhibitors have been approved for the clinic. Thus, there is still room in the field for the development of a safe therapeutic target that can effectively block this process. There is a consensus in the literature that PtdSer is critical for KRAS anchoring to the membrane, and this paper describes how MTMR proteins may impact the supply of PtdSer to the PM. Since this work is done in a cancer background by utilizing a mutant KRAS construct (KRASG12V), this work would be interesting to many cancer researchers that are attempting to target mutant KRAS. This paper would also be interesting to researchers who investigate mechanisms of PM maintenance.

      Our lab studies RAS signaling in tumorigenesis. The authors are clear in their explanations of the mechanisms of PM maintenance and PM components relevant to this study.

    1. Keyword

      En otros Lenguajes de programación este mensaje estaría representado de la siguiente manera:

      ``` 4.estaEntre(0.10)

      ``` o podría ser algo como

      ``` compararNumeroEntre(4,0,10)

      ```

    2. Character space

      Al conjunto de todos los caracteres, es decir Character, le estamos enviando el mensajes space, lo cual nos entrega un conjunto dentro de ese conjunto. En este caso, estamos enviando el mensaje a un conjunto, lo cual se reconoce porque su primera letra es mayúscula. Si fuera minúscula, se la estaria enviando a un elemento de un conjunto. A los conjuntos se les conoce como clases, a los elementos se les conoce como instancias.

      A veces puede pasar que le enviemos un mensaje a una clase o una instancia y que el resultado caiga en otra instancia.

      1 to: 10

    1. Los mensajes 'keyword' son mensajes con argumentos. Tienen la siguiente forma: anObject akey: anotherObject akey2: anotherObject2 Inspecciona los siguientes mensajes keyword: 4 between: 0 and: 10.

      En otros lenguajes de programación, este mensaje estaría representado de la siguiente manera:

      Por ejemplo Ruby 4.estaEntre(0,10)

      o podría ser algo como:

      compararNumeroEntre(4,0,10)

    1. Author Response

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

      Reviewer #1

      Weaknesses:

      Start site fidelity in purified recons5tuted systems can be drama5cally altered in different buffer condi5ons. Interpreta5on of the observed changes to start site selec5on in mRNAs in the absence or presence of Ded1 using only the one buffer condi5on used is therefore limited.

      This is an excellent point and is something we could explore in future studies using the Rec-Seq system. We have added this caveat to the Discussion on lines 797-809. We have previously studied the fidelity of start codon recogni>on in the recons>tuted system (Kolitz et al., [2009] RNA, 15:138-152) and found that under our standard buffer condi>ons the codon specificity generally reflects what we observed in vivo using a dual-luciferase reporter assay, with the most stable 48S complexes forming on AUG codons, followed by first posi>on mismatches (GUG, UUG, CUG), with second and third posi>on mismatches leading to significantly less stable complexes. However, as the reviewer notes, there are some devia>ons: ACG and AUA are poor codons in the in vitro system under the buffer condi>ons used but allowed rela>vely strong expression in our in vivo reporter assay. It should also be noted that the hierarchy of nearcognate start codon usage in vivo in yeast differs according to the study and the reporter used, making it difficult to establish a “ground truth” for start codon fidelity.

      I have some specific comments to strengthen the manuscript and address some minor issues.

      It is not clear to me whether the authors refold the purified mRNA aEer phenol/chloroform extrac5on? Have the authors observed different results if the mRNA is refolded or not? This is appropriate since the authors compare their Rec-Seq data to PARS scores that were generated from refolded mRNAs. One assumes that the total mRNA used is refolded in the same way as the PARS score study, but this is not clearly stated. The authors should make this point clear in the text and methods.

      This is an excellent point. We did not use the final refolding protocol that Kertesz et al. used when they developed their PARS scores and now clarify this in the Methods sec>on (lines 962967). It is possible that we would have seen stronger correla>ons in the analyses using PARS scores had we followed the renatura>on protocol, although the fact that we observed significant correla>ons (e.g., Fig. 3E-H) suggests the structures in the Kertesz et al. mRNAs were similar to those in our mRNAs.

      It is not clear how the authors determine the concentra5on of total mRNA that is used in the assay - reported as 60 nM? Are the authors assuming a molecular weight of an average mRNA to determine the concentra5on? The authors should provide more detail for how they quan5fy their mRNA concentra5on and its stoichiometry compared to 43S PICs.

      We thank the reviewer for poin>ng out this oversight and have now included this informa>on on lines 849-855 of the Methods sec>on.

      Comments regarding start site fidelity in the recons5tuted system:

      The authors use in vitro transcribed tRNAi-Met. Since tRNA modifica5ons may play a role in start site fidelity, the authors should perhaps men5on that this will need to be inves5gated in a future study in the discussion.

      This is a good point and we now note it as a caveat in the Discussion on lines 806-809.

      The authors state that Ded1 promotes leaky scanning regardless of the mAUG start site context (page 24; lines 533-534). The authors then state on page 25 that the level of iAUG ini5a5on rela5ve to mAUG ini5a5on does depend on the mAUG context (lines 545-546). This seems contradictory unless I am not understanding this correctly? It would certainly be surprising that mAUG context didn't regulate leaky scanning in the recons5tuted system given the fact that ini5a5on codon context regulates selec5on in cells (when Ded1 is present).

      These statements are correct as wrihen. As shown in Figure 5O, the frequency of leaky scanning (as measured by rela>ve ribosome occupancy of the internal region of the ORF, not including the main start codon, to the whole ORF, including the main start codon; RRO) decreases as the context score around the start codon gets stronger (green and purple lines). The RRO is increased to the same extent when 500 nM Ded1 is added, regardless of the strength of the start codon context, indica>ng that Ded1 enhances leaky scanning equally (compare slopes of the green line without Ded1 to the purple line with Ded1). Because of this, the effect of Ded1 on RRO (DRR0) is constant across context score bins (orange line). There is no discrepancy between our two conclusions that leaky scanning of the mAUG increases as context score decreases and that Ded1 increases leaky scanning equally for good and bad mAUG contexts, indica>ng that Ded1 does not inspect the mAUG context and simply decreases the dwell >me equally at all contexts.

      Further to the start site context ques5on. It is possible that the fidelity of the recons5tuted system (i.e. buffer condi5ons) is not fully reflec5ng in vivo-like start site selec5on. A rigorous characteriza5on of commercially available re5culocyte lysate systems iden5fied buffer condi5ons that provided similar start site fidelity to that observed in live cells (Kozak. Nucleic Acids Res. 1990 May 11;18(9):2828). While I feel that it is beyond the context of the current work to undertake a similar rigorous buffer characteriza5on, one must be careful about interpre5ng the results about leaky scanning and upstream ini5a5on sites in the current work. Perhaps one would observe similar results to Guenther et al. if the fidelity (buffer condi5ons) of the recons5tuted system were different? I appreciate that the authors state that their results only apply to their recons5tuted system and do not necessarily suggest that previous data are incorrect, but with only one buffer condi5on being tested in the current study it may be appropriate to further soEen the interpreta5on of the current results when compared to published data in live cells.

      This point is well-taken. As noted above, we have added a caveat about possible effects of buffer condi>ons on start codon fidelity to the Discussion (lines 797-809). In terms of the possibility that upstream ini>a>on is more frequent in vivo than we observe in the in vitro RecSeq system, we previously studied 5’UTR transla>on in vivo using ribosome profiling (Kulkarni et al. [2019] BMC Biol., 17:101). The ra>o of RPFs in 5’UTRs to coding sequences in this study was 0.0027, very similar to the value measured in the in vitro Rec-Seq system in the presence of Ded1 (0.0016-0.0017). Thus, it does not seem that the frequency of upstream ini>a>on is drama>cally higher in vivo than in our in vitro system. We have now made note of this point in the Results (lines 594-598). Guenther et al. employed a ribosome profiling protocol in which they added cycloheximide to their cells prior to lysis, which has been shown to create significant ar>facts, par>cularly in 5’UTR transla>on (e.g., Gerashchenko and Gladyshev [2014] Nucleic Acids Res., 42:e134). Nevertheless, as suggested by the reviewer, we have modified the text in the Results and Discussion to somen the interpreta>on somewhat (lines 582-583; 616-618; 761763).

      Reviewer #2

      Weaknesses:

      Several findings in this report are quite surprising and may require addi5onal work to fully interpret. Primary among these is the finding that Ded1p s5mulates accumula5on of PICs at internal site in mRNA coding sequences at an incidence of up to ~50%. The physiological relevance of this is unclear.

      We agree with the reviewer that understanding the physiological significance, if any, of the apparent leaky scanning of main AUG start codons induced by Ded1 is an unanswered ques>on that will require addi>onal studies. It is possible that rapid 60S subunit joining and forma>on of the 80S ini>a>on complex amer start codon recogni>on on most mRNAs reduces the leaky scanning effect in vivo. We now bring up this possibility in the Discussion sec>on (lines 804809). However, as noted in lines 568-580, mRNAs that display significantly decreased mRPFs at 500 nM Ded1 in the Rec-Seq system also tend to have TEs that are increased in the ded1-cs- mutant rela>ve to WT yeast in in vivo ribosome profiling experiments, sugges>ng that Ded1 ac>vity also diminishes ini>a>on on mAUG codons in these mRNAs in vivo.

      A limita5on of the methodology is that, as an endpoint assay, Rec-Seq does not readily decouple effects of Ded1p on PIC-mRNA loading from those on the subsequent scanning step where the PIC locates the start codon. Considering that Ded1p ac5vity may influence each of these ini5a5on steps through dis5nct mechanisms - i.e., binding to the mRNA cap-recogni5on factor eIF4F, or direct mRNA interac5on outside eIF4F - addi5onal studies may be needed to gain deeper mechanis5c insights.

      We agree that this is a limita>on of the Rec-Seq assay and now men>on this point in the Discussion sec>on (lines 810-817). It is possible that future work using cross-linking agents to stabilize 43S complexes bound near the cap and scanning the 5’UTR, similar to the methodology used in 40S ribosome profiling, could enable us or others to disentangle these steps from one another.

      As the authors note, the achievable Ded1p concentra5ons in Rec-Seq may mask poten5al effects of Ded1p-based granule forma5on on transla5on ini5a5on. Addi5onal factors present in the cell could poten5ally also promote this mechanism. Consequently, the results do not fully rule out granule forma5on as a poten5al parallel Ded1p-mediated transla5on-inhibitory mechanism in cells.

      We agree. As stated in the Discussion sec>on (lines 735-741): “It is possible that at higher concentra>ons of Ded1 than were achievable in these in vitro experiments or in the presence of addi>onal factors that modify Ded1’s ATPase or RNA binding ac>vi>es the factor could directly inhibit a subset of mRNAs, by ac>ng as an mRNA clamp that impedes scanning by the PIC, or by sequestering the mRNAs in insoluble condensates. It might be interes>ng in the future to test candidate factors in Rec-Seq to determine if they switch Ded1 from being a s>mulatory helicase to an inhibitory mRNA clamp that removes transcripts from the soluble phase.”

      It is certainly clear why the 15-minute 5mepoint was chosen for these assays. However, I wondered whether data from an earlier 5mepoint would provide useful informa5on. The descrip5on on line 210 of the compiled PDF suggests data from different 5mepoints may be available; if it is, in my view it could be a useful addi5on. More generally, including language about the single-turnover nature of these reac5ons may be helpful for the benefit of a broad audience.

      In preliminary experiments, we have used the Rec-Seq system to measure the kine>cs of 48S PIC forma>on transcriptome-wide. As you probably can imagine, this is a challenging experiment and requires addi>onal work before we would feel comfortable publishing it. We very much agree with the reviewer that resolving the kine>cs of these events will provide important addi>onal informa>on. As suggested, we have added caveats about the endpoint and single-turnover nature of the assay to the Discussion (lines 821-828).

      I wondered whether it might be useful to present addi5onal informa5on on the mRNAs not found in the assay. For example, are these the least abundant mRNAs, which may not have had 5me to recruit the 43S PIC?

      75% of mRNAs (2719 of 3640) not observed in the Rec-Seq analysis had densi>es below the median (2.3 reads per nucleo>de). We now men>on this in the Methods sec>on (lines 855856).

      The Rec-Seq recruitment reac5ons were carried out at 22C˚ . Considering that remodeling of RNA structure by helicase enzymes is a focal point of the study, linking the results to the recruitment landscape at a closer-to-physiological temperature may bolster the conclusions.

      In the future, it would be interes>ng to test the effects of temperature on 48S PIC forma>on using the Rec-Seq system. As the reviewer suggests, the interplay between temperature and mRNA structure could reveal interes>ng phenomenon. It is worth no>ng, however, that there is no clear “physiological” temperature for S. cerevisiae. For consistency and convenience, lab yeast is usually grown at 30 ˚C, but in the wild yeast live at a wide range of temperatures, which generally change throughout the day. From this standpoint, 22 ˚C seems reasonably physiological.

      Results from Rec-seq experiments conducted at 15° C might be more directly comparable to in vivo Ribo-seq data with the ded1-cs mutant. However, already ~90% of the Ded1hyperdependent mRNAs iden>fied by Ribo-seq analysis of that mutant were iden>fied here as Ded1-s>mulated mRNAs in Rec-Seq experiments at 22°C. The Ribo-seq experiments conducted by Guenther et al. were conducted on the ded1-ts mutant at 37°C; thus, any structures that confer Ded1-dependent leaky-scanning through uORFs detected in that study should have been stable in our Rec-Seq experiments.

      The introduc5on provides an important, detailed exposi5on of the state of the field with respect to Ded1p ac5vity. Nevertheless, in my view, it is quite lengthy and could be streamlined for clarity. As just one example, the proposed func5on of Ded1p in the nucleus seems like a detail that could be dispensed with for the present work.

      We have ahempted to shorten the Introduc>on, as suggested. However, we did not remove the short sec>on describing Ded1’s possible roles in the nucleus and ribosome biogenesis because we felt it was important to emphasize that one of the strengths of the Rec-Seq system is that it allows us to isolate the early steps of transla>on ini>a>on from later steps and from other cellular processes. In addi>on, at the sugges>on of Reviewer #3, we added a brief explana>on of Ded1’s possible role in the subunit joining step of transla>on.

      Reviewer #3

      Weaknesses:

      The slow nature of the biochemical experiments could bias results.

      We agree that the 15-minute >me point used could mask effects that are manifested at a purely kine>c level. It should be noted that we have measured the observed rate constants for 48S forma>on on a variety of mRNAs in the in vitro recons>tuted system in the presence of satura>ng Ded1 (Gupta et al. [2018] eLife, hhps://elifesciences.org/ar>cles/38892 ) and found that they are generally in the range of es>mates of rate constants for transla>on ini>a>on in vivo in yeast (~1-10 min-1; e.g., Siwiak and Zielenkiewicz [2010], PLOS Comput. Biol., 6: e100865). In preliminary experiments, we have used the Rec-Seq system to measure the kine>cs of 48S PIC forma>on transcriptome-wide in the absence of Ded1 and find that the mean rate constant observed (~2 min-1) is also within the range of es>mates of the rate of transla>on ini>a>on in vivo in yeast. We hope to publish this analysis in a future manuscript.

      It has been suggested that Ded1 and its human homolog DDX3X could play a role in subunit joining postscanning (Wang et al. 2022, Cell and Geissler et al. 2012 Nucleic Acids Res). Could the authors poten5ally inves5gate this by adding GTP, eIF5B and 60S subunits into the reac5on mixture and isola5ng 80S complexes?

      This is a very interes>ng sugges>on. One of our plans with the Rec-Seq system is to see if we can also observe 80S forma>on with it and dis>nguish 80S from 48S complexes. Although we haven’t yet tried this and there might be technical obstacles to doing it, if it works we would like to examine the poten>al effects of Ded1, as suggested. We now men>on this possibility in the Discussion sec>on (lines 709-716 and 810-817).

      An incuba5on 5me of 15 minutes is quite long on the 5mescale of transla5on ini5a5on. Presumably, the compe55on for 40S among mRNAs is par5ally kine5cally controlled so it would be interes5ng if the authors could do a 5me series on the incuba5on 5me. Does Ded1 increase ini5a5on on more structured UTRs even at shorter incuba5ons or are those only observed with longer incuba5ons?

      We agree. See the response to the ques5on about kine5cs above.

      Does GDPNP lead to off-pathway events? What happens when GTP is used in the TC? Presumably in the absence of eIF5B the 48S PIC should remain stalled at the start codon.

      In previous experiments in the recons>tuted system, we showed that using GTP instead of GDPNP resulted in 48S complexes that were less stable than those stalled prior to GTP hydrolysis (e.g., Algire et al. [2002] RNA 8:382-397). This is presumably because eIF2•GDP and eIF5 release from the complex and the Met-tRNAi can dissociate in the absence of subunit joining. Although we haven’t tried it in the Rec-Seq system, we suspect that the resul>ng PICs would fall apart during sucrose gradient sedimenta>on.

      The authors use assembly of a 48S PIC at the start codon as evidence of scanning but could use more evidence to back this claim up. Does removing the cap structure on the two luciferase mRNA controls disrupt ini5a5on using this approach? That would be direct evidence of 5' end 40S loading and scanning to the start codon.

      In previous work using the recons>tuted system, we studied the effect of the 5’-cap on 48S PIC forma>on (Mitchell et al. [2010] Mol. Cell 39:950-962; Yourik et al. [2017] eLife hhps://elifesciences.org/ar>cles/31476 ). We found that stable 48S PIC forma>on is strongly dependent on the presence of the 5’-cap. In addi>on, the cap prevents off-pathway events and enforces a requirement for the full set of ini>a>on factors to achieve efficient 48S PIC forma>on. As the reviewer indicates, the cap-dependence of the system supports the conclusion that 5’end loading and scanning take place. We have now added this informa>on and the relevant cita>ons to the Introduc>on (lines 147-153). We thank the reviewer for poin>ng out this oversight. It should also be noted that the cases of mRNAs in which 5’UTR transla>on is increased by addi>on of Ded1 support the conclusion that the factor promotes ahachment of the PIC to the 5’ ends of mRNAs and subsequent 5’ to 3’ scanning, as noted in lines 608-618.

      The authors state that "The correla5on between CDS length and RE could be indirect because CDS length also correlates with 5'UTR length". Could the authors bin the transcripts into different 5' UTR length ranges and then probe for CDS length differences on RE for each 5' UTR length bin? This could be useful to truly parse the mechanism by which CDS length is influencing RE.

      This was an excellent sugges>on. We now include this analysis in a new supplementary figure, Figure 3S-2. Corresponding text was added in lines 380-387:

      “Importantly, correlations between Ded1 stimulation and 5’ UTR lengths are evident for all three groups of mRNAs containing distinct ranges of CDS lengths (Fig. 3-S2A-C). In contrast, a marked correlation between Ded1 stimulation and CDS length was detected only for the group of mRNAs with longest 5’UTRs (Fig. 3-S2D-F), and only the latter group showed a clear correlation between 5’UTR length and CDS length (Fig. 3-S2G-I). Thus, the correlation between Ded1 stimulation and CDS length appears to be indirect, driven by the tendency for the mRNAs with the longest 5’UTRs to also have correspondingly longer CDSs.”

      We thank the reviewer for this very useful idea.

      In Figure 3I, why does RE dip for the middle bins of CDS length in both 100 nM and 500 nM condi5ons, and then rise back up for the later bins? In other words, why do the shortest and longest CDS have the best RE in the presence of ded1?

      We do not know the reason for this dip and now say this in the Results on lines 377-378.

      The discussion sec5on would be well served to discuss proposed roles of Ded1 post-scanning and how those fit, if at all, with the data presented throughout the manuscript.

      We have now added this to the Discussion (lines 709-716 and 810-817). We thank the reviewer for poin>ng out this oversight.

      Minor comments:

      • Define bins on figures rather than using bin number for axis labels. For example, Figure 3A-D x-axis labels indicate the length range of each bin.

      Thank you for the sugges>on. We have made this change.

      • Figure 3I: the data seem to indicate that shortest CDSs have a ded1 dependency similar to the longest CDSs. This result seems inconsistent with the given rela5onship between UTR length, structure, CDS length. Please clarify.

      See answer to this ques>on above.

      • Replace qualita5ve statements, such as "substan5ally smaller reduc5ons" with percent change, numbers, etc.

      We have tried to replace qualita>ve statements with quan>ta>ve ones, where possible.

    1. En el músculo estriado, hay otras dos proteínas que son menores en términos de su masa pero importantes en su función. La tropomiosina, presente en todos los músculos y estructuras similares a músculos, es una molécula fibrosa que consta de dos cadenas, α y β. Las cadenas se adhieren a la actina F en el surco entre sus filamentos (figura 51–3). El complejo de la troponina es exclusivo del músculo estriado y consta de tres polipéptidos. La troponina T (TpT) se une a la tropomiosina así como a los otros dos componentes de la troponina. La troponina I (TpI) inhibe la interacción actina F-miosina y también se enlaza a los otros componentes de la troponina. La troponina C (TpC) es un polipéptido fijador de calcio cuya estructura y función son análogas a la calmodulina, una notable proteína fijadora de calcio de amplia distribución en la naturaleza. Se pueden unir hasta cuatro iones de calcio por molécula de troponina C o calmodulina.

      n

    1. Além disso, quando você inicia o Git na pasta raiz de um projeto, o RStudio criará uma nova abinha chamada Git, onde você pode confirir os arquivos modificados que estão à espera de um commit.

      colcar no GIT

    1. decreto,

      Estado de defsa: presidente, ouvidos o conselho da república e da defesa nacional. Ordem pública ou a paz social = locais restritos e determinados. MEDIANTE DECRETO.

    1. but the musicwill not comeif you are afraidmusic like most things in life enters in only one of two waysel amor o el dolor through love or through pain

      through music/ creativity we are able to express our joy and our pain

    2. but the musicwill not comeif you are afraidmusic like most things in life enters in only one of two waysel amor o el dolor through love or through pain

      love this qoute el amor o el dolor

    1. Of this new world; at whose sight all the starsHide their diminished heads; to thee I call,But with no friendly voice, and add thy name0 Sun, to tell thee how I hate thy beams

      Stars often symbolize guidance and hope in poetry, with this line tying into "O Sun." We often see the Sun representing God's influence and power. These ideas surrounding authoritative guidance reveals a sign of submission after trial. In a way it seems as if one has given up and is throwing a white flag to a form of structured guidance.

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      Referee #3

      Evidence, reproducibility and clarity

      Summary:

      Provide a short summary of the findings and key conclusions (including methodology and model system(s) where appropriate). Please place your comments about significance in section 2.

      In the manuscript "Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis" the authors investigate the TRAPPII interactome carried out by an already published IP-MS screen. They study previously identified shaggy-like kinases SK as TRAPII interactors and the phosphorylation sites by Y2H (interactions of wild type, deletion mutants and phosphomutants) and kinase assays (in vitro) and pharmacological inhibition in the subunit AtTRS120. The authors provide a deeper phenotypical analysis of trapii null mutant lines and classification as "decision mutants", based on "limited budget" and "conflict of interest" experiments (previously described) as a starting point of investigations of TGN function in comparison with hormone mutants. Cell elongation is used as a response phenotype. Authors focus on mainly TRS120 and phosphorylation by SK and partly on another TRAPP component, CLUB. Authors study the assays with differing kinases, e.g. Y2H with BIN2, phosphorylation with SK11.

      Major comments:

      • Are the claims and the conclusions supported by the data or do they require additional experiments or analyses to support them?

      A major issue is that new claims and conclusions are not supported by the new data provided here. The title says "in Arabidopsis", but only components are from Arabidopsis. Interactions, instead, are studied in this manuscript by Y2H in yeast, and phosphorylation in vitro. The abstract is very misleading and does not distinguish which aspects are studied in vitro and which in vivo. The Abstract does not mention that this study is based on previously identified interactome data.

      o The figure legends are often not sufficiently detailed to understand what exactly is represented.

      Therefore, it is not possible to judge in every case whether experiments are supported by data. E.g.

      Fig. 1: A, describe which data were used and which control for IP-MS had been taken into account. B, this is a plot, please describe what is represented. Explain better why Shaggy kinases were chosen. C, explain the principle and what is represented. How is this experiment controlled and how is it ensured that negative results are not caused by absent proteins.

      Fig. 2: Indicate the phosphorylation sites in the other subfigures. Fig. 2E: How was it generated, explain what is seen. Since this is the only figure illustrating the protein complex of TRAPP, this figure should be more thoroughly prepared and labeled. I recommend a better visualized protein complex. As before, Fig. 2F remains unclear.

      Fig. 3: Please add a figure illustrating the mutations. 3C: what has been diluted? Other examples are found in other figures.

      Fig. 4: Shouldn't the wild type be compared with all the mutants? Then statistics have to be conducted accordingly. Better explain G and H. If there are quotients, explain of what exactly.

      Fig. 5. Same as before. How do I see that there is a phenotype? There is no comparison with wild type. It is also unclear to which values the statistics refer to.

      Fig. 6: Please guide the reader through the figure and experiment.

      Fig. 8: I miss the connection with other shaggy-like kinases. This summary could be more complete. What about phosphorylation sites?

      o Line 133-134: "we focus on the TRAPPII complex as a starting point as it is required for all aspects of TGN function, including the sorting of proteins such as PINs to distinct membrane domains" I did not find an obvious connection to the PIN transporters as well as clear data to TGN functions. This sentence was for me misleading about the context of this manuscript.

      o Figure 1C: A supporting Western Blot control is needed, to fully validate the missing interaction of BIN2 with the truncated variants of TRS120 and CLUB. Additionally, swapping the constructs from DB to AD and vice versa will provide a better set-up of the interaction screen. This should be easily done in a few weeks.

      o Line 431-432: "This presents intriguing implications regarding the potential role of the AtSK-TRAPPII module in meeting the unique demands of endomembrane traffic in plants." Why do the authors come to this assumption? Further discussion is needed here.

      o Figure 2F: What serves as positive controls? What is the purpose of showing every panel between each TRS120-T2 variant with CLUB-C2, CLUB-C3, TRS120-T1 and TRS120-T3 and not only interactions between BIN2 and the TRS120-T2 variants? Why are there six negative controls as it is every time the same control? - Please request additional experiments only if they are essential for the conclusions. Alternatively, ask the authors to qualify their claims as preliminary or speculative, or to remove them altogether.

      Clearly, title, abstract and statements have to be formulated differently. The discussion should contain a limitations paragraph in which the authors detail that conclusions are based on in vitro, yeast and plant IP-MS screening data, and they should describe approaches how the study can be continued in the future. Which alternative explanations are possible. Are SKs and TRAPP expressed and present in the same locations? - If you have constructive further reaching suggestions that could significantly improve the study but would open new lines of investigations, please label them as "OPTIONAL". - Demonstrating interactions and phosphorylation by other approaches in vivo - demonstrating effects of TRAPP phosphomutants and lack of kinases in vivo - Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated time investment for substantial experiments. - Are the data and the methods presented in such a way that they can be reproduced?

      o Figure S9: Is it not a loss of chlorophyll instead of GFP? Does not look like a fluorescent image.

      o Lacking information of pH of in vitro kinase assay solution with Mass-spectrometry.

      o What is the purpose of transferring 10 days old seedlings to fresh plates for scanning? Needs additional information for understanding, at the moment it sounds more like unnecessary extra stress for the seedlings.

      o Why are seedlings grown under constant light? - Are the experiments adequately replicated and statistical analysis adequate?

      o Figure 5: It will be good to use ANOVA for statistics here. I personally doubt the high significance of some parameters, e.g. for club-2 cell width and cell surface area between dark and darkW due to the high standard errors. Rechecking with the original values is necessary. Why is there no comparison between wild-type and the two mutants?

      o Figure 7A - C, statistic is probably not correct. For example: in A statistical differences with P<0.001 between wild-type (~100 %) and TRS120SαβγD (~80 %), in C statistical difference of only P<0.05 between wild-type type (90 %) and TRS120SαβγD (60 %)

      o No information on IP-MS replicate numbers mentioned.

      o Also see comments above to figures

      Minor comments:

      • Specific experimental issues that are easily addressable.
        • Specific experimental issues that are easily addressable.

      o Figure 4, S7, S8, S11 and S12: It will be helpful to support the data with images of the seedlings. - Are the text and figures clear and accurate? Do you have suggestions that would help the authors improve the presentation of their data and conclusions?

      o The introduction is quite lengthy with unnecessary information, e.g. about PIN transporters, but useful information about shaggy-like kinases and connection to brassinosteroid signaling is lacking.

      o Figure 1C: In the figure legend is no explanation of abbreviation "Co"; no explanation of BET3, TRS31, Tca17 and TRIPP; no indication that spots come from different plates (just visible by different brightness of the squares). Why are there eleven negative controls as it is every time the same control?

      o Figure 1C is specifically for BIN2, but BIN2 was not identified in the IP-MS screen represented in Figure 1B. Why does 1C not focus on SK11/12/32, identified in 1B?

      o Figure 1C shows several truncated variants of TRS120 and CLUB, a schematic overview as represented in Figure 2A will be helpful for the understanding of 1C. Order of variants should be the same (now: in 1C first TRS than CLUB in 2A first CLUB than TRS).

      o Figure 1C: Interaction of TRS120 full-length with BIN2 is missing in this figure but is presented in Figure 2F.

      o Result of Figure 2F is described after Figure 3. Better arrangement of Figures or text is needed here.

      o Figure 3A: Why was AtSK11 and not BIN2 used for the main figure? Better change Figure 3A with Figure S4 to keep the focus on BIN2. No explanation of the result in the text.

      o Figure 3A: In the figure legend is no explanation of abbreviation CBB. What are the non-phosporylated variants? Where are they shown? Description sounds that only TRS120-T2-SαβγA versus TRS120-T2 WT was tested by t-test is this correct? And if yes, why?

      o No need for Figure 3B, information was already given in Figure 2A + B.

      o Figure 3C: Why BIL2 for Clade II and not BIN2?

      o Figure 4: Why are A-E not directly compared to wild-type but trs120-4 as seen in 4F? What is the purpose of using different types of diagram?

      o Figure 4H: Why are phyAphyBcry1cry2 and pyrpyl1pyl2pyl4 depicted? No description in the text.

      o Figure 6: Confusing order of given information in the figure legend. Sentence one belongs to D and H only, second sentence describes whole figure. o Figure 6D + H, color difference between black and blue is hard to see, better change one into e.g. red.

      o Figure 7D - F wrong indication of D to F, named in the description as A) - C). Why is E different to D in F (D and F: 0-1 is attenuated, >1 enhanced; E the other way around).

      o Figure S9A: Indication of protein size on the Coomassie gel is missing and the respective position of 160 kDa is not visible on the gel.

      o Figure S12D: No explanation of the color code in the figure legend.

      o Consistent labelling and layout of all Figures and Supplemental Figures will be helpful. E.g., Figure 3A and S4; in S8A-E + S11A-C bars of different conditions have the same color. Most of the figure legends are quite shortly described and lack information about what kind of data is presented.

      o YFP parameters are described in material and methods, but no YFP construct appeared in the manuscript to my knowledge. - Are prior studies referenced appropriately? - Lines 243-245: Text is nearly identical to Kalbfuß et al., 2022. - Lines 246-254: Text is identical to Kalbfuß et al., 2022. - Are the text and figures clear and accurate?

      Please see the above and below comments to figures and figure legends. - Do you have suggestions that would help the authors improve the presentation of their data and conclusions?

      Overall, the manuscript may have very interesting data and new findings. It is very interesting that the authors study the regulation of a protein complex that may mediate environment responses and intracellular Golgi functions. However, it is very difficult to follow and understand the ideas and concept of the manuscript. This manuscript is based on a previously published interactome study by Rybek et al. 2014, Steiner et al. 2016, Kalde et al. 209. Moreover, a physiological approach is published in Kalbfuß et al. 2022. The outcomes and conclusions from these previously published manuscripts and the emanating open questions addressed here should be clearly described in the introduction. This is currently not the case. Moreover, many experimental approaches and results (e.g. figures, figure legends) are not properly described. Overall, it is therefore not possible to understand the manuscript without studying in depth all other manuscripts. Before the manuscript can be more thoroughly judged, it is necessary that the authors rewrite the manuscript, reorganize it and explain better their ideas and approaches. It is also necessary to explain and define unusual terms such as "decision mutants", "limited budget" and "conflict of interest" experiments, which are crucial for the understanding. The importance of the TRAPPII complex should be illustrated using specific physiological examples and the context in which this complex is studied here has to be explained. Before this is not corrected, the following assessment will remain rather incomplete. Another complication is that two subunits of TRAPP were studied and different types of SKs, however, authors did not systematically analyze all interactions. At least it should be thoroughly described, and a flow chart would be helpful as supplemental figure clearly describe which types of proteins were tested in the different assays. The introduction is not well written. It is very lengthy, however the important messages from previous publications are left out. Thus the open question is not understandable (see above). Instead, the results parts start with introduction again. Explanations are also lacking in every result paragraph on the approach and expected data. The Discussion is also not very well written. It is much focused on physiological and molecular actions and consequences in plants. However, there should be at first a technical discussion on the relevance since in the study is based on in vitro and heterologous expression data, and the physiological analysis was only conducted with knockouts but not phosphomutants. Therefore, the link between the protein interaction and physiological functions needs to be worked out.

      Referees cross-commenting

      My colleague and I have read thoroughly the manuscript and found a number of issues which we indicated in our review. These points can be fixed by the authors, if they formulate more carefully and remove the overstatements. They should also work on reorganizing and including more explanations.

      Significance

      Provide contextual information to readers (editors and researchers) about the novelty of the study, its value for the field and the communities that might be interested.

      The following aspects are important:

      One new aspect of this story is the validation of interaction of TRAPII subunits as substrate for AtSKs and their action as phosphorylation agents shown in vitro. The other new aspect is the phenotypical characterization of trapii mutants under stress-conditions (grown in darkness) and additive stress (with additional drought stress). The potential interaction with brassinosteroid signaling via BIN2 is intriguing.

      • General assessment: provide a summary of the strengths and limitations of the study. What are the strongest and most important aspects? What aspects of the study should be improved or could be developed? A strength is that a new interaction is further studied. A weakness is that the studies are primarily conducted in yeast and in vitro, leaving open how relevant this process is in plants. A strength is further studies and phenotypic analysis of trapii mutant effects. A weakness is that this mutant analysis is disconnected from the action of SKs.

      Further, the writing should be improved and more clear (see comments above). - Advance: compare the study to the closest related results in the literature or highlight results reported for the first time to your knowledge; does the study extend the knowledge in the field and in which way? Describe the nature of the advance and the resulting insights (for example: conceptual, technical, clinical, mechanistic, functional,...). The introduction gives the impression of a stronger investigation of TGN function, which is from my point of view not the case and should be reformulated and/or put into a deeper context with known literature. The authors switch several times between the different TRAPPII subunits and shaggy-like kinases in the main figures which made it for me very confusing. I believe that rearranging some data/figures will improve the understanding of the story. The text is also lacking explanations of many abbreviations and gene names which caused more difficulties in understanding the story and slowed down the reviewing process. From my point of view it seems to be necessary to read the often cited Kalbfuß et al., 2022 publication before, as many important technical aspects and scientific background, e.g. the reason to use specific control mutants, are well explained there, but are lacking in this manuscript and needs improvement. - Audience: describe the type of audience ("specialized", "broad", "basic research", "translational/clinical", etc...) that will be interested or influenced by this research; how will this research be used by others; will it be of interest beyond the specific field? Based on the cited literature in this manuscript the direction of the story with "limited budget" and "conflict of interest" situations to classify mutants methodically seems to be a recently emerged approach. Apart from that this manuscript provides only new impact on TRAPII and AtSKs specific knowledge based on well-established and frequently used techniques that address the problem in vitro and in a heterologous system. Therefore, this story will be interesting for researchers specialized in stress responses, TGN and growth defects as well as important for basic research. Limitations in interpretation are present. - Please define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.

      Our field of research is related to nutrition-regulated processes especially in Arabidopsis with a strong methodological background in interactomics, physiological, morphological and molecular responses and biochemical approaches and microscopy.

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      Reply to the reviewers

      Review Commons Refereed Preprint #RC-2023-02149

      Dear Reviewers #1 and #2,

      We extend our deepest gratitude for your dedication to reviewing our manuscript during such a busy period. We have diligently addressed the insightful feedback provided in our revisions. The variable quality of human fetal tissues, due to fixation and extended preservation times, is acknowledged as a limitation that may affect the quality of our immunostaining results. Despite this, we maintain that the findings from these experiments are crucial for human applications. The extrapolation of the results from mice experiments to human biology is a critical step in propelling research forward. We are confident that our paper, with its acknowledged limitations, still offers valuable contributions to our understanding in this domain.

      Please find the primary amendments of our revision detailed below for your review.


      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      Summary Yamaguchi et al. performed a comprehensive characterisation of lymphatic vessel development in human embryos, spanning stages C8 to GW9. Through the utilisation of immunohistochemistry targeting proteins expressed in the lymphatic endothelium and blood endothelium, the authors have discerned the presence of lymphatic endothelial cells within the cardinal vein and in extraveinal locations. By systematically analysing the progression of embryonic stages, the authors identified the emergence of lymph sacs. Furthermore, they confirmed the presence of lymphatics in various organs, such as the heart, kidney, lung, and mesentery. However, lymphatics were not detected in the central nervous system during the embryonic stages. At the molecular level, lymphatic endothelial cells express similar factors as in mice, including Prox1, Vegfr3, Lyve1, and PDPN, although the timing and combination of these factors may vary depending on the tissue. This study significantly contributes to our knowledge of lymphatic development in humans.

      Major comments Human embryo samples are exceptionally valuable and ethically sensitive, making their maximum utilisation crucial. While the authors conducted a thorough anatomical and molecular analysis, it raises questions about whether more insights can be gleaned.

      Specifically, the authors should clarify whether data from embryos collected at CS8-CS10 were processed, and what was the status of venous and lymphatic development?

      Response: After a careful review of the clinical data for the specimen previously classified as CS8, we found a record indicating the initial detection of a heartbeat in the preceding week, an observation not made earlier. When correlating the last menstrual period with the morphological features, such as the open neural tube, it suggests that the specimen may actually be at CS 9-10, rather than CS8. We have revised the details in our records to reflect this more accurate staging in Table 1. We have included sections of this particular specimen for Figures for reviewer 1. Despite exhaustive sectioning until the sample was depleted, the heart structure was not located. The developmental stage of the specimen seems comparable to that of a mouse embryo at approximately embryonic day 7.5, evidenced by what appears to be a caudal neuropore. In addition, we observed surrounding blood vessels expressing PECAM, which contained nucleated red blood cells, but these did not exhibit Prox1 expression.

      Figure for reviewer 1. Prox1 Expression Pattern in a CS9-10 Human Embryo.

      Cross-section of a CS9-10 human embryo. Immunostaining for PECAM and Prox1.

      The authors commented that CS11 lymphatic vessels were not identified in the vein. Was there any indication of LECs outside the vein? Could the authors include images of this stage?

      Response: The CS11 embryo is depicted in Supplemental Figure 2A-C’. In this section, identification of one side of the precardinal vein was possible. Furthermore, formation of the pharyngeal arch was observed. Prox1 expression was absent in the precardinal vein at this stage.

      For embryos at CS12, it would be insightful to know the proportion of LECs versus VECs within the vein, the quantity of LECs outside the veins, and whether there was section-dependent variability in these observations. Response:

      For a single section, the numerical data for the right and left anterior cardinal veins were averaged. This process was repeated and the results were then averaged across two sections.

      1. The proportion of LECs to VECs within the vein. On average, there were 18.25 nuclei per cross-section of the CV; of these, 4.5 were Prox1-/PECAM+ blood endothelial cells (BECs), and 13.75 were Prox1+/PECAM+ LECs. Therefore, BECs constituted 24.7%, and LECs constituted 75.3%.

      The number of LECs outside the veins.

      There were an average of 9.75 Prox1+/PECAM+ cells located externally to the CV."

      This point is described in Figure 1 legends as follows.

      On average, there were 18.25 nuclei per cross-section of the CV; of these, 4.5 were Prox1-/PECAM+ blood endothelial cells (BECs), and 13.75 were Prox1+/PECAM+ LECs. Therefore, BECs constituted 24.7%, and LECs constituted 75.3%. There were an average of 9.75 Prox1+/PECAM+ cells located externally to the CV. (Page 11, lines 486-490)

      It would be helpful if Table 1, "Information of human embryos and fetuses", could be complemented with a summary of the main findings at each stage, including which markers LECs expressed and their distribution.

      To strengthen the assertion that this study provides unique insights compared to those of mice, a schematic summarizing the similarities and differences between mouse and human observations should be included. Response:

      We have enriched the information presented in Table 1 and introduced Figure 5 as a new comprehensive illustration. Figure 5 provides a comparative analysis of lymphatic vessel development between mice and humans, with a particular emphasis on the early stages of development, meticulously summarizing the alterations in lymphatic marker expression at specific stages.

      The authors mentioned differences in lymphatic markers at various regions of the embryo and different developmental stages. It is essential to clarify whether all regions express the same markers at the latest developmental stage. Response:

      We have added immunostaining for Podoplanin and LYVE1 at GW9 as Supplemental Figure 4X-Y''. This demonstrates the expression of Podoplanin and LYVE1 in lymphatic vessels of the lung, heart, kidney, mesentery, intestinal wall, and lower jaw. This information regarding the expression of LYVE1 and PDPN has also been incorporated into the main body of the text under the section of ‘The Development of Lymphatic Vessels Varies Among Organs’.

      A discussion of the limitations of analysing embryos from abnormal pregnancies is necessary. In addition to the determined lack of chromosomal abnormalities, it is crucial to consider phenotypical and morphological integrity. The authors should address the possibility of developmental defects and mutations causing abnormalities in the lymphatic vessels.

      Response:

      In the "Tissue Collection and Ethical Considerations" section of the Materials and Methods, we have addressed the possibility that developmental defects and mutations may cause abnormalities in the lymphatic vessels.

      This is depicted as follows:

      Detailed information regarding each sample is presented in Table 1. The sex of each sample was not determined, with the exception of one case of miscarriage. In this particular case, chromosomal analysis verified the absence of any karyotypic abnormalities. There were no malformations observed in any of the embryos or fetuses. Nevertheless, for the remaining embryos, there is a possibility that developmental defects or mutations could lead to abnormalities in the lymphatic vessels. (Page 7, lines340-346)

      Minor comments In the abstract, the authors refer to lymphatic malformations as a specific type of lymphatic disease. We recommend acknowledging the broader implications of this study beyond such specific cases. 

      Response:

      We have modified the concluding paragraph of the Abstract to reflect a more expansive and encompassing narrative as follows.

      Our research clarifies the early development of human lymphatic vessels, contributing to a better understanding of the evolution and phylogenetic relationships of lymphatic systems, and enriching our knowledge of the role of lymphatics in various human diseases. (Page2, lines 58-60)

      The term "lymph-related disease" should be clarified for better understanding. Response:

      To make it clearer, we have modified the last paragraph of the Introduction that includes 'lymph-related disease' as follows.

      Our research offers essential insights into the evolution and phylogeny of lymphatic vessels, and may also illuminate the pathogenesis of lymphatic-related diseases, which include lymphedema, obesity, cardiovascular disorders, Crohn's disease, and congenital lymphatic disease, such as lymphatic malformation. (Page 3, lines127-131)

      Figure 3S shows kidney samples, not the myocardium or endocardium, as indicated. Response:

      No, it is correct. Figure 3P-S represents the heart, which is surrounded by the lungs on both sides. Figure 3S depicts the endocardium, indicating that lymphatic vessels are not present within the endocardial layer.

      Reviewer #1 (Significance (Required)):

      This study largely reaffirms the existing knowledge from mouse models and previous human data. Given the absence of a cure for lymphatic diseases, gaining a deeper understanding of how lymphatic vessels develop in humans could serve as a crucial stepping stone in this field of research.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      This study by Yamaguchi et al., explores the progression of lymphatic vessel growth in different stages of human embryos. They also try to identify the origin of the lymphatic vessels in different organs. The study first shows that lymphatic endothelial cells (LECs) first show up in the anterior cardinal veins (ACVs) of CS12 in human embryos, which is similar to what is known to occur in mouse embryos. They also checked whether the PROX1+ LECs of the heart are derived from Flk1+/Isl+/PECAM- cells. However, Flk1+/Isl+/PECAM- cells do not co-express PROX1. These results suggest that in human embryos LECs originate from the ACVs. The authors then identify that lympho-venous valves formed between lymph sacs and the cardinal veins at around Carnegie Stage (CS)18. The valves have showed obvious bicuspid shape at Gestational week (GW)9. Finally, the authors demonstrate that the development of lymphatic vessels happens at different time points in various organs. At CS16, lymphatic vessels and LECs can be detected in the lower jaw, heart and the lungs; mesenteric and intestinal lymphatic vessels can be detected between CS17 and CS18; kidney lymphatic vessels can be found at CS23; At GW9, the lymphatic vessels are observed around the aorta, which may combine to form the future thoracic duct. Together, this informative study sheds light on the progression of lymphatic vasculatures during embryonic stage in humans.

      This study has many strengths, in addition to some areas that if addressed, would further increase the impact of the findings. These include:

      1. Since immunostaining is the major method that the authors have used for their work, they could use positive and negative controls (secondary antibody only or IgG control) for different antibodies. The authors can also show some Isl1 and Flk1 staining in GW9 fetus or adult tissue, like PROX1 or LYVE1 in Supplemental figure 1.

      Response:

      We have introduced new Supplemental Figures 1I-N. Included are negative controls for fluorescent staining with only the secondary antibody (Supplemental Figure I-I’’’’) and for DAB staining with only the secondary antibody (Supplemental Figure J-L). Furthermore, we have added images showing Flk1 staining within lymph sacs (Supplemental Figure 1M) and Isl1 staining (Supplemental Figure 1N). Flk1 expression was confirmed in the lymph sacs; however, Isl1 expression was not observed.

      The description regarding the negative controls is as follows.

      Additionally, the specificity of the staining was confirmed with controls using only the secondary antibodies (Supplemental Figure 1I-L). (Page 3, lines146-147)

      The description regarding Flk1 and Isl1 in the lymph sac is as follows.

      Additionally, at GW9, Flk1 expression was detected in the cervical lymph sac, but Isl1 expression was not (Supplemental Figure 1M and N). (Page4, lines186-187)

      Figures 1 F-H, S' and S", U', U", and U'" are hard to appreciate. Can the authors offer higher quality images or show some confocal images?

      Response:

      In response to the reviewer's comments, we conducted several trials to improve image quality. However, due to fixation issues, we were unable to enhance the quality beyond the original for the CS12 specimen. Therefore, all images except those of VEGFR3 have been left unchanged. It is possible that the quality appeared reduced in the initial submission due to compression, making them difficult to view. We will resubmit without reducing the image quality as much as possible and ask for your understanding in this matter. Additionally, the CS12 specimen was very small, and there was a limited number of sections available, making further attempts challenging. This is also a limitation of research using human embryos. Regarding Figure 1R-U’’’, we have revised and replaced the images, although the quality has not significantly changed. We believe this may also be due to the compression of the image quality at the time of submission. There is no change in the conclusions drawn.

      According to the author's previous publications (ref 17 and 30) and literature (ref 31), Flk+/Isl+/PECAM- cells differentiate into LECs. However, in this work they did not observe any PROX1+Isl1+ cells at CS13 and CS14. I am curious to know if they found any PROX1+Isl1+ cells at later time points such as GW9.

      Response:

      Isl1 is posited to be an early transcription factor that directs the differentiation of undifferentiated mesodermal cells towards a cardiac lineage. Our prior research utilizing tamoxifen-inducible mice indicated that a cohort of cells expressing Isl1 at a defined interval (E6.5 to E9.5 in mice) contributes to the formation of lymphatic structures in the head, neck, mediastinum, and heart before subsequently losing this expression(Maruyama et al., eLife, 2022). However, in human studies, it is not possible to trace the lineage and differentiation trajectories of Isl1+ cells. Consequently, we anticipated finding LECs that initially express Isl1 in the embryonic stage, with this expression diminishing as development ensues. Nevertheless, such cell groups were not observed in human embryos. In mice, our search for cells concurrently expressing Isl1, Prox1, Flk1, or PECAM from E9.0 to E11.5 (referenced in Maruyama et al., eLife, 2022, Supplemental Figure 3) also yielded no such populations. This evidence suggests that Isl1 protein expression in the cardiac pharyngeal mesoderm likely ceases during the differentiation into lymphatic endothelium. Given the hypothesis that Isl1+/Prox1+ LECs might exist at an earlier developmental stage, we examined specimens from CS16, 17, and 18 for the presence of such LECs but to no avail. This investigation has been documented as Supplemental Figure 3Q-S for the CS16 sample. With the GW9 sample, due to its substantial size, we initially conducted a DAB staining search for lumen structures that might express Isl1. However, no such structures were identified. Moreover, despite conducting triple immunostaining for PECAM, Isl1, and Prox1, we were unable to locate any LECs or lymphatic vessels expressing Isl1.

      The description regarding Isl1 and Prox1 expression for CS16 and GW9 is as follows:

      At CS16, cells co-expressing Prox1 and Isl1 were not observed in the lower jaw or the cardiac outflow tract regions (Supplemental Figure 3Q-S'). Additionally, at GW9, Flk1 expression was detected in the cervical lymph sac, but Isl1 expression was not (Supplemental Figure 1M and N). (Page 4, lines184-187)

      For the GW9 stage, we have provided images of lymphatic vessels in the lung and heart stained with PECAM, Isl1, and Prox1 as a Figure for the reviewer's consideration.

      Figure for reviewer 2. Isl1 is not expressed in GW9 lymphatic vessels.

      Fluorescent immunostaining of PECAM, Prox1, and VEGFR3 was conducted at GW 9 fetuses. Scale bars 100μm.

      Figure 3 N and O show comparable VEGFR3+PROX1+ cell numbers in different time points, however it shows increased VEGFR3+PROX1+ vessel numbers. If so, do LECs become more elongated and form the vessel-like structures?

      Response:

      In our previous findings (Maruyama et al., Dev bio, 2019, Maruyama et al., iScience, 2021), we documented that surrounding the heart, LECs progressively interconnect to form a reticular network, which is subsequently remodeled into more substantial lumen-bearing vessels. This sequence appears to be conserved in humans, with LECs initially presenting as solitary entities that gradually interlace into a network. Presumably, a portion of this network is then streamlined, giving rise to increasingly luminal structures. Therefore, while the count of LECs remains constant, there is an augmentation in the number of defined luminal vessels. This observation has been depicted as follows.

      Throughout this process, the initially mesh-like capillary lymphatics undergo progressive remodeling to establish lumen-bearing vessels. Consequently, while the density of LECs per unit area remains relatively stable, there is an increase in the number of lymphatic vessels possessing distinct luminal structures (Figure 3N and O). (Page 5, lines 220-223)

      The authors have mentioned that the staging of the embryos and fetuses was done by Carnegie stage and clinical information. The authors should offer more detailed information about those embryos and fetuses. For example, crown-rump length, menstrual weeks, craniofacial features etc. This information will be useful for other researchers in this field.

      Reply:

      We have substantially expanded the data presented in Table 1 regarding embryos and fetuses. For specimens dating back over 15 years, some lacked echo graphic details. In those instances, we estimated the developmental stage by integrating available data, such as the date of the last menstrual period or morphological features of the fetus. For a case initially assessed as CS 8, which had no recorded cardiac activity in the preceding week, a subsequent ultrasound noted a heartbeat. Considering this alongside the specimen's size, we revised the estimated stage to CS 9-10, correlating with the onset of heart formation. Despite exhaustive sectioning of this particular embryo until the samples were depleted, the heart structure remained undetected. Nevertheless, taking into account morphological observations, such as an open neural tube, the stage was adjudged to be CS9-10. Furthermore, for ectopic pregnancies, which frequently necessitated emergency surgeries due to symptoms like abdominal pain or bleeding, preoperative embryonic data was often unavailable.

      Reviewer #2 (Significance (Required)):

      Strengths: Very informative results for human embryonic lymphatic development. They have performed the experiments at various developmental stages.

      Limitations: Image quality need to be improved. Many high magnification images are not clear. Human samples come from certain diseases, which might have affected the embryo's development.

      Advance: this study clarified the process of early lymphatic vessel formation in human embryos.

      Audience: clinical and basic science in developmental biology and lymphatic biology.

      Reviewer expertise: lymphatic development, lymphatic biology, vascular biology.

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      Referee #2

      Evidence, reproducibility and clarity

      This study by Yamaguchi et al., explores the progression of lymphatic vessel growth in different stages of human embryos. They also try to identify the origin of the lymphatic vessels in different organs. The study first shows that lymphatic endothelial cells (LECs) first show up in the anterior cardinal veins (ACVs) of CS12 in human embryos, which is similar to what is known to occur in mouse embryos. They also checked whether the PROX1+ LECs of the heart are derived from Flk1+/Isl+/PECAM- cells. However, Flk1+/Isl+/PECAM- cells do not co-express PROX1. These results suggest that in human embryos LECs originate from the ACVs. The authors then identify that lympho-venous valves formed between lymph sacs and the cardinal veins at around Carnegie Stage (CS)18. The valves have showed obvious bicuspid shape at Gestational week (GW)9. Finally, the authors demonstrate that the development of lymphatic vessels happens at different time points in various organs. At CS16, lymphatic vessels and LECs can be detected in the lower jaw, heart and the lungs; mesenteric and intestinal lymphatic vessels can be detected between CS17 and CS18; kidney lymphatic vessels can be found at CS23; At GW9, the lymphatic vessels are observed around the aorta, which may combine to form the future thoracic duct. Together, this informative study sheds light on the progression of lymphatic vasculatures during embryonic stage in humans.

      This study has many strengths, in addition to some areas that if addressed, would further increase the impact of the findings. These include:

      1. Since immunostaining is the major method that the authors have used for their work, they could use positive and negative controls (secondary antibody only or IgG control) for different antibodies. The authors can also show some Isl1 and Flk1 staining in GW9 fetus or adult tissue, like PROX1 or LYVE1 in Supplemental figure 1.
      2. Figures 1 F-H, S' and S", U', U", and U'" are hard to appreciate. Can the authors offer higher quality images or show some confocal images?
      3. According to the author's previous publications (ref 17 and 30) and literature (ref 31), Flk+/Isl+/PECAM- cells differentiate into LECs. However, in this work they did not observe any PROX1+Isl1+ cells at CS13 and CS14. I am curious to know if they found any PROX1+Isl1+ cells at later time points such as GW9.
      4. Figure 3 N and O show comparable VEGFR3+PROX1+ cell numbers in different time points, however it shows increased VEGFR3+PROX1+ vessel numbers. If so, do LECs become more elongated and form the vessel-like structures?
      5. The authors have mentioned that the staging of the embryos and fetuses was done by Carnegie stage and clinical information. The authors should offer more detailed information about those embryos and fetuses. For example, crown-rump length, menstrual weeks, craniofacial features etc. This information will be useful for other researchers in this field.

      Significance

      Strengths: Very informative results for human embryonic lymphatic development. They have performed the experiments at various developmental stages.

      Limitations: Image quality need to be improved. Many high magnification images are not clear. Human samples come from certain diseases, which might have affected the embryo's development.

      Advance: this study clarified the process of early lymphatic vessel formation in human embryos.

      Audience: clinical and basic science in developmental biology and lymphatic biology.

      Reviewer expertise: lymphatic development, lymphatic biology, vascular biology.

    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

      We thank the reviewers for their comments and constructive criticisms of the manuscript. We thank them for positive comments on the high quality of the genetic screen and recognizing our contributions in respect of RDGB work in Drosophila.

      In general, there is one important comment by the reviewers about the candidates identified in the proteomic screen as potential VAP interactors which have then been tested in the genetic screen. Reviewers have noted that many proteins in the proteomics study identified as VAP interactors do not have the classical FFAT motif that mediates VAP interaction. Therefore, what is the significance of such genes?

      Response: It is important to reflect on the fact that while VAP interacts with FFAT motifs in proteins , a VAP immunoprecipitation will identify two classes of proteins (i) those with classical FFAT motifs (ii) those proteins without FFAT motifs that interact indirectly with VAP via proteins which themselves have FFAT motifs. We have already depicted this in Fig 2A as category C proteins.

      We believe that the in vivo genetic screen does in fact serve the specific purpose of testing the functional significance of such non-FFAT containing proteins identified in the proteomic screen by functional validation of their ability to modulate rdgB degeneration.

      Key modifications to the text and a few experiments planned are listed in the next sections against pointwise response to reviewer comments. We believe that this will strengthen the manuscript.

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      Mishra and colleagues have conducted a large genetic screen to identify modulators of a Drosophila model for retinal degeneration. Using biomolecular techniques, they selected a few hundred proteins that interact with an ER bound protein VAP, to further test them in the retinal degeneration model. This was done by downregulating their expression using interference RNA (RNAi). Degeneration was first measured through a pseudopupil analysis, then suppressors of degeneration were further tested in a different retinal degeneration model, and finally through an ERG experiment. Finally, they focused on a strong suppressor of degeneration, dCert, by using a mutant allele to confirm the findings from the RNAi. The results suggest that a handful of these candidates are suppressors in this model of retinal degeneration, and identify at which stage of retinal degeneration these proteins may be involved in. These proteins may have a significance in forms of neurodegeneration.

      Major comment: - Perhaps a larger number of replicates could be done in the optical neutralization experiment as well as in the ERG. Figure 4.A(i) and (ii), please clearly state n values. I would suggest this as optional, but perhaps ut could help to increase n?

      Each optical neutralization experiment was done using 5 independent animals and 10 ommatidia were scored from each animal. For the optical neutralization experiment in 4.A(i) and (ii) we did 5 independent animals with 10 ommatidia/ animal for the statistical score. Based on our past experience, this number is sufficient to capture the intra-ommatidial variability in each eye and the inter animal variability between animals. This information will be added to the figure legend.

      For the ERGs minimum 5 animals were used per experiment which is already mentioned in the figure legend and conforms to the standards of analysis in the field for such experiments.<br /> - For human orthologs (Table 1), it could be worthwhile to add alignment scores between fly and human?

      We will add the table with the alignment score

      Minor comment: - Clarify the purpose in focusing on dCert specifically in the last results section and discussion - Several typos - Affect vs effect

      • Following the initial genetic screen, it was necessary to characterize a genes to understand in detail the temporal and spatial aspects of it role in modulating degeneration. Dcert was chosen for several reasons (i) a classical germ line mutant allele was available (ii) Prior papers had established its role as a protein that functions at contact sites. We will clarify our purpose of including dCert as proof of principle in the discussion part.

      -Typos will be corrected.

      Reviewer #1 (Significance (Required)):

      General assessment:

      The main significance of this study comes from the focus on proteins that are known to interact with VAP. This implies that the suppressors of degeneration that they have identified in the RdgB9 model may have an effect in other neurodegenerative models, namely in ALS models. This could have a very high significant potential in therapeutic avenues for neurodegenerative diseases.

      Among six candidates that had an effect with knocked down through RNAi, they pursued a single one (dCert) as proof of principle. It would help to add a justification for this choice in the main text and whether the authors have performed or intend to perform experiments using mutant forms of the other candidate proteins.

      Although six candidate genes were available for analysis, there were no mutants available in two of them (SET and CG3071). Mutants in Yeti are homozygous lethal making it difficult to work on it in this setting. However a viable mutant in APC is now available and a CG9205 CRISPR germ line deletion mutant has recently been generated in our lab. We will use these two alleles to test their, interaction with rdgB like we did for dcert. Since dCert and CG9205 have membrane interacting domains we prefer to focused on these two genes for this study as proof of principle.

      The work from Raghu and his team have been leading the research surrounding this model of degeneration in Drosophila. This study naturally further extends their field of research, identifying more candidates that modulate this form of degeneration, and helping elucidate the pathways leading to cellular degeneration.

      These results will be of high interest for specialized researchers studying the molecular pathways that lead to cellular degeneration, both in the context of retinal degeneration as well as neurodegeneration. Specifically, researchers that may be interested in these candidate proteins and how they may play a role in the pathogenesis of various degenerative diseases.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Summary: In this study, Mishra and colleagues combine proteomic techniques with Drosophila genetics to identify interactors of the endoplasmic reticulum (ER) protein VAP and analyse their indirect implication in the light-dependent retinal degeneration phenotype caused by misfunction of the lipid transfer protein RdgB, another VAP interactor. This is an ideal model system to study neurodegeneration in vivo via which the authors aim to further understand the molecular mechanisms involved in VAP-RdgB's function in maintenance of membrane lipid homeostasis. Of an initial list of 403 VAP mammalian interactors found via Immunoprecipitation - Mass Spectromety performed in a human cell line, 52 homologous Drosophila genes are found to suppress the RdgB degeneration phenotype upon knockdown. The authors then test a series of genetic interactions to dissect the potential role of these genes in the degeneration phenotype and identify six genes that likely suppress the phenotype by directly acting on the same molecular processes as RdgB, two of which (Cert and CG9205) could have a direct mechanistic role in the lipid homeostasis maintained by the VAP-RdgB complex.

      Major comments: - The model suggested by the authors in Fig 2A is one by which the tested genes influence the VAP-RdgB function via direct binding to VAP. The direct interaction with VAP is a core aspect of the study as the IP-MS experiment biases the list of genes tested in Drosophila, and this list is often referred to as "VAP interacting proteins". However, the interactions between the proteins coded by the most relevant genes in the genetic screen and VAP are not tested. In fact, of the six genes that are found to likely modulate the same processes as RdgB, four probably do so via affecting gene expression, as discussed by the authors, therefore making it unlikely that they are true VAP interactors (unless they shuttle from the ER to the nucleus). Additionally, it would seem that most of the 52 genes found to suppress the degeneration phenotype are not necessarily VAP interactors either as only a handful of genes in this list have predicted strong FFAT motifs. In general, the authors should provide additional comments/evidence on the interaction, or likelihood of the interaction, of these proteins with VAP, that should include: o The IP-MS data should be made available (at least on my end, in the current submission the supplementary lists available cover only the 52 genes found to suppress the phenotype, I found the list of 403 genes in the biorXiv submission but this also does not include data on the enrichment of each hit in the IP-MS). It should be made clear how enriched were each of the proteins in the analysis, and how high the most relevant genes in the genetic screen rank within this interactor list.

      We will provide more details on the MS data. We can add the ratio (VAP WT vs VAP mutant) and the PSM, number of peptides etc in the table, and we will deposit the raw data on PRIDE repository.

      It is true that some of the genetic interactors, especially those that do not have an obvious FFAT motif likely influence the retinal degeneration phenotype either by indirect interactions with VAP or functional interactions rather than structural interaction. This point can be emphasized in the discussion. It is important to note that this is in some senses a good reason to couple of protein interaction screen with a genetic screen., the genetic screen sometimes uncovering functional interactions via indirect mechanism. The likely mode of interaction can be made clear in a revision.

      o The authors should provide further detail on the rationale behind defining the list of 403 genes to be tested (for example, what was the threshold enrichment considered as interaction). Also in relation to this, the authors should at least provide speculation as to why more than half of the 403 genes defined do not have an FFAT motif, despite the fact that the proteomic data was normalized to a non-FFAT motif binding mutant of VAP which should be capable of maintaining non-FFAT mediated interactions of the protein.

      As the reviewer correctly mentions, the 403 genes from the proteomics screen used for the genetic screen all satisfied the criterion of being differentially enriched in binding seen to wild type VAP but not the non-binding version of VAP. This is despite that fact that many of these proteins do not have an identifiable FFAT motif. The reason for this is most likely that the candidates without the FFAT motif most likely bind to VAP indirectly via a protein which itself has an FFAT motif. This is depicted in Figure 2A. This has already been explained in the text but this can be elaborated further.

      The rationale for including candidates from the proteomic screen without an FFAT motif in the genetic screen is that we were interested in all candidates that might influence RDGB function whether they are direct or indirect binders of VAP.

      o The authors should acknowledge the limitations of their experimental design in regards to identifying real interactors of VAP in Drosophila and avoid referring to this set of genes as "VAP interacting proteins" and rather use a more accurate description such as "proteins enriched in the IP-MS" or at least "potential VAP interacting proteins".

      We agree that the use of ‘potential VAP interactors’ may be more appropriate.

      o Testing interaction between VAP and all the 52 genes found to suppress the phenotype would be a huge amount of work. But the finding most relevant to the initial premise of the study (i.e. "molecular mechanisms underlying lipid transfer protein function at membrane contact sites") is that Cert (a lipid transfer protein) and CG9205 (fly homolog of a mammalian lipid transfer protein) influence RdgB function. Demonstrating an interaction between these proteins and VAP would argue for the experimental design and support the hypothesis and model of the study. Cert is already a well established interactor of VAP, hence the authors would not need to add anything regarding this protein. Is CG9205 expected to be also a true interactor of VAP? Biochemical experiments could be used to test this idea, or even recently developed in silico modelling of interactions (i.e. AlphaFold Multimer) could be of help. If no interaction is observed/expected this should also be pointed out in the manuscript. Optionally, showing localization of Cert or CG9205 to the ER-PM interface would also greatly support the model of VAP-RdgB regulation suggested by the authors.

      We agree that further experimental evidence to support the interaction of CG9205 would add useful information. This can be attempted by co-IP or by in silico methods such as Alpha fold multimer.

      Minor comments: - In the model shown in Fig2A, it would seem that many proteins can bind VAP in addition to RdgB, however, VAP proteins have only one FFAT binding pocket. This model would only be possible if oligomerization of VAP is considered (oligomerization of VAP has been reported to occur, see for example PMID:20207736). The model should be redrawn considering this fact.

      We agree.

      • In line 161 of the text VPS13D is mentioned, however VPS13C is the gene indicated in Fig 1D.

      The text will be corrected.

      Reviewer #2 (Significance (Required)):

      Previous studies by some of the authors and others have shown that RdgB can transfer lipids between the ER, to which it binds via VAP, and the plasma membrane (PM), and is required for proper replenishment of PI(4,5)P2 in the PM which is in turn necessary for sustained PLC signaling in Drosophila photoreceptors. Lack of RdgB leads to light-dependent degeneration of the retina, and hence it is utilized by the authors as a model for neurodegeneration. Given the clear phenotype of RdgB loss-of-function and the ease of Drosophila genetics, this system represents an ideal model to perform screens for the identification of new genes involved in maintaining neuronal lipid homeostasis required for proper function of the photoreceptors in vivo, and this aspect is the main strength of this study. Importantly, the use of this system could also shed light on the mechanisms behind human neurodegenerative disorders, as many of these involve dysregulation of lipid signaling and lipid transfer at membrane contact sites. A novel and interesting finding is the identification of another lipid transfer protein, Cert, to be involved in the degeneration of photoreceptors.

      The main limitation lies in the experimental design proposed by the authors to define the genes that are studied in their system. These are identified as potential interactors of human VAP in a mammalian cell line. Despite the fact that VAP is a highly conserved protein, and the genes identified are present in Drosophila as well, there is no evidence that these interactions are in fact occurring in Drosophila photoreceptors, and in fact, based on the function and the lack of VAP-binding motif in many of the 52 genes identified to have an effect on the RdgB phenotype, it is likely that many of the interactions are purely genetic and indirect, and that the modulation of the phenotype could in fact be due to a wide variety of factors (including, as discussed by the authors, gene expression, post-translational modifications, trafficking of proteins, etc) unrelated to mechanisms of VAP-RdgB mediated lipid transfer at ER-PM membrane contact sites.

      A more unbiased screen could have been carried out to identify VAP interactors involved in this degeneration phenotype by testing all of the FFAT or FFAT-related motif containing proteins. Due to this initial bias in the selection of genes to be tested, it is possible that other important VAP interactors that play a role at the ER-PM interface of photoreceptors have not been identified.

      We agree that an alternative approach might have been to perform the VAP interaction proteomics in fly photoreceptors rather than start with a proteomics data set from mammalian cells. At this late stage in the project this will not be a feasible approach. However, we could consider testing any FFAT containing proteins, identified bioinformatically in the fly genome in the future.

      An initial bioinformatics analysis has revelated that there are only 51 genes in the entire fly genome with an identifiable conventional FFAT motif. Of these 7 are already part of the genetic screen already completed. Of the remaining 44 genes, 11 show no expression in the eye and 9 show very low expression. Thus, using the approach suggested by the reviewer ca. 24 genes with FFAT motifs could have been missed and therefore could be screened, subject to genetic tools, i.e RNAi lines being available for these.

      This study provides great functional advance in the understanding of genes implicated in photoreceptor degeneration, and in those regards it is a great resource for a specialized audience, as it enables further characterization by others of the different processes implicated in this neurodegeneration phenotype. However, the advance is small in regards to the core mechanism of RdgB function at VAP-mediated ER-PM, which was the main aim of the article and the most broadly interesting aspect of the study. Many of the VAP-interacting proteins identified in the proteomic approach were already expected to be VAP interactors as they contain FFAT motifs, and these FFAT-containing proteins do not seem to have a major role in VAP-RdgB maintenance of neuronal lipid homeostasis, with the exception of Cert. The implication of Cert in RdgB-mediated lipid homeostasis is certainly interesting as it touches on a current topic in the field of membrane contact sites related to how the multiple interactions of VAP, a universal contact site adaptor at the ER, are regulated and influenced by each other.

      Reviewer's field of expertise: Lipid transfer at membrane contact sites; membrane lipid homeostasis in neurons. All of the Drosophila data seem to be of good general quality to me, but I do not have any expertise in Drosophila work.

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      Reply to the reviewers

      Manuscript number: RC-2023-02012

      Corresponding author(s): Frederic, Berger

      [Please use this template only if the submitted manuscript should be considered by the affiliate journal as a full revision in response to the points raised by the reviewers.

      If you wish to submit a preliminary revision with a revision plan, please use our "Revision Plan" template. It is important to use the appropriate template to clearly inform the editors of your intentions.]

      1. General Statements [optional]

      This section is optional. Insert here any general statements you wish to make about the goal of the study or about the reviews.

      We thank reviewers for useful suggestions and comments on our manuscript which helped to improve and strengthen our conclusions. Our point-by-point answers are below. We have answered most of the points raised by the reviewers and added numerous new experimental data including detailed structural and biochemical analyses that led to support further that BCP4 (and not BCP3) is the plant functional counterpart of MDC1 because in response to DNA damage it binds phosphorylated H2A.X and recruits the MRN complex. In addition, we provide further support to the phylogenetic analysis and evidence for the plant counterpart of PAXIP1.

      We believe that our revised manuscript which includes a set of new experimental data strongly support our main conclusion that BCP4 is a functional counterpart of metazoan MDC1.

      2. Point-by-point description of the revisions

      This section is mandatory. *Please insert a point-by-point reply describing the revisions that were already carried out and included in the transferred manuscript. *


      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      MDC1 is a key regulator of DNA damage responses (DDR) in animals. MDC1 has multiple protein domains, in which the BRCT domain binds γH2A.X. However, plants lack the homolog of MDC1. In this study, the authors found that BCP4 binds γH2A.X and proposed that BCP4 is a functional counterpart of MDC1, which will greatly enhance our understanding of plant DDR pathway. I have the following concerns.

      1. The relationship between BCP3 and BCP4 needs to be clarified. Line 255, the authors mentioned that"we conclude that BCP3 and BCP4 have functional properties as human MDC1". In the Abstract, the authors mentioned that "we identified BCP4 as a candidate ortholog of human MDC1". I am confused about the conclusion. Both BCP3 and BCP4 are or only BCP4 is MDC1? In addition, in BCP3 and BCP4, only their BRCT domains share homology with MDC1. They lack other domains of MDC1. Therefore, "ortholog" may not be an appropriate term. I think "functional counterpart" may be a better term.

      Response: Our analysis emphasizes the fact that human MDC1 is very derived from an ancestral form MDC1 that did not share most domains found in MDC1 from mammals. Because it is still difficult to establish with certainly what the ancestral MDC1 was, we agree that functional counterpart is a more correct term, so we changed this accordingly throughout the manuscript.

      BCP1-4 all contains tandem BRCT domains. I am wondering whether it is possible to figure out why only BCP3 and BCP4 bind γH2A.X through sequence analysis. Are there any key residues essential for γH2A.X binding?

      Response: We used AlphaFold models of tBRCT domain of BCP1, BCP2, BCP3, and BCP4. While in Alphafold models the tBRCT domain of each BCP protein largely overlaps with a structure of human MDC1 tBRCT domain, only the tBRCT domain of BCP3 and BCP4 are predicted to make contacts with γH2A.X similar to that of human MDC1. Although residues that are involved are not fully conserved between BCP3/4 and human MDC1 we obtain in vitro data supporting that the interaction of BCP4 is mediated by a comparable pocket of three key residues that contact the phosphate group of γH2A.X. See also answers to comments of Referee #2 and new Figures 3 and 4, corresponding description on page 8-9, and Supporting figure 3.

      Line 183, "On an unrooted phylogenetic tree, these two proteins clustered with MDC1 and PAXIP1 (Figure 1B).". In Figure 1B, MDC1 is closer to BCP3 and BCP4 than PAXIP1 and PAXIP1 is closer to BCP2 than MDC1. If the authors want to include PAXIP1 in Figure 1C, the authors should include BCP2 as well. In the γH2A.X binding assays, I do not understand why the authors tested BCP1 instead of BCP2. In Figure 2D, why bcp2 was not included?

      Response: We created a new alignment for Figure 1C including BCP2 tBRCT domain and the tree that includes all BCP BRCT domain (Figure 1D) does support a close relation between MDC1 and BCP3 and 4 and PAXIP1 and BCP1. As we stated on page 5-6 lines 175-178, BCP2, also contains acetyltransferase domain, which is unique for plant BCP2 protein. Based on its domain organization, BCP2 was not considered as a candidate for MDC1 homolog, and we did not perform mutant complementation. This is why after our initial analysis of bcp mutants (DNA damage sensitivity, formation of gammaH2A.X, and phylogeny), and based on similarities with MDC1 and PAXIP1 we focused on bcp1, 3, and 4 mutants and the corresponding proteins. The function of BCP2 remains to be investigated, but this is out of the scope of this manuscript that is primarily dedicated to find the functional counterparts of MDC1 and PAXIP1.

      The expression level of BCP1-4 in the mutants need to be examined using qRT-PCR. Especially, for the bcp3 mutant, which is a weak allele.

      Response: We did not perform this experiment, because it was done in Vladejic et al., 2022 and expression data are available from various genomic dataset on TAIR.

      The authors used "bleomycin" or "zeocin" in different parts. Please be consistent.

      Response: We consistently use Bleomycin for treatment of seedlings followed by western blotting and Zeocin for true leaf assay. These two agents produce DNA double strand brakes in similar ways, and we could show previously that levels of γH2A.X and γH2A.W.7 are similar when using these two agents (Rosa M, Mittelsten Scheid O Bio. Protoc. 4:e1093. doi: 10.21769/BioProtoc.1093: Lorkovic et al., Curr Biol. 2017, doi: 10.1016/j.cub.2017.03.002). Zeocin was chosen for true leaf assays because we observe lower variation between batches and biological repeats compared with bleomycin.

      1. Figure 3E and 3F, please indicate the treatments of the upper and lower panels.

      Response: Thank you for pointing this out. This has been indicated in the corresponding legend of the new Figure 3 A - C.

      Line 338, "bcp1 mutants show reduced homologous recombination rates (Fan et al., 2022; Vladejić et al., 2022; Yu et al., 2023)". The bcp1 mutant was not reported in Fan et al. paper.

      Response: This sentence has been changed to accurately describe data in each of the mentioned papers.

      Line 40, please add a comma after "In ". Line 331, please add a comma after "In mammals". animal

      Response: This has been corrected.

      Line 123, "only BRCA1 and BARD1 were described in plant lineage". Additional BRCT proteins were described in plants, including XIP1 (Nat. Commun. 13:7942), BCP1/DDRM2 (New Phytol. 238:1073-1084; Front. Plant Sci. 13:1023358), and DDRM1 (PNAS, 119: e2202970119).

      Response: This sentence refers to known BRCT domain mediator/effector proteins. From the published data about XIP1, BCP1/DDRM2, and DDRM1, it is not possible to assign these functions to proteins in question. Nevertheless, we changed this sentence to avoid ambiguous interpretation and we later in the text introduce XIP1, BCP1/DDRM2, and DDRM1 proteins as needed.

      Reviewer #1 (Significance (Required)):

      This study identified BCP4 as a functional counterpart of MDC1, which filled the gap of plant DDR signaling.

      __Reviewer #2 (Evidence, reproducibility and clarity (Required)): __ In this study, Frédéric Berger and colleagues identified BCP4 in Arabidopsis thaliana as a potential plant orthologue of vertebrate MDC1. The conclusions are based on both in silico analysis (phylogenetic analysis) and in vitro biochemical and cell biological experiments. BCP4 loss causes sensitivity of DNA damage. Moreover, BCP4 binds to a phosphopeptide derived from the C-terminus of H2AX, via its C-terminal BRCT domains and forms foci in cells exposed to DNA damage, which co-localize with gammaH2AX foci.

      Major comments: The conclusions are generally supported by the data, but the evidence presented is still quite limited. For example, it is still possible that BCP4 recruitment to sites of DNA damage is mediated by another protein and not by direct interaction with gammaH2AX. To firmly conclude that BCP4 is an MDC1 orthologue, it is in my opinion essential to perform a (limited) mutagenesis analysis. The key amino acids in the BRCT domains that recognize gammaH2AX need to be mutated and it has to be shown that these mutants are defective for H2AX phosphopeptide binding and are not recruited to sites of DNA damage. Such residues may be tricky to identify, but one obvious candidate would be the Ser residue in beta1 (VLFS motif). In vertebrates, this is a Thr that directly interacts with the phosphate in gammaH2AX. Another possible critical site may be shortly before alpha2 (RTRN motif). In vertebrates, it is RTVK, and the K makes direct contacts with the phosphate in gammaH2AX. This function is perhaps carried out by an R. Structure prediction with alphafold may help to identify the most critical residues

      Response: We thank the reviewer for these suggestions. We used AphaFold to predict structures of tBRCT domains of all BCPproteins and compared them with structure of human MDC1 in complex with gamaH2A.X peptide. Based on these analyses we performed mutagenesis of critical amino acids in BCP4 based on their predicted interaction and their conservation. We showed that mutations of critical residues reduced or almost completely abolished binding of BCP4 to γH2A.X. These data are now part of the new Figure 4. See also corresponding description on page 8-9. In addition we provide genetic data that show that the foci formation of BCP4 depends on H2A.X (new Fig 3B and C). We did not attempt genetic complementation experiments with these mutants because it would take nine months to obtain stable transgenic plant lines expressing various mutant versions of BCP4 and the limitation of Arabidopsis transgenesis does not allow to control precisely the expression of transgenes, which could cause a difficult interpretation in this particular case.

      Another critical issue is the introduction of the study. This needs to be revised, because the literature is not correctly cited in several places. For example, the cited paper by Salguero et al., 2019 did not show that the PST repeats of MDC1 constitute a docking site of TP53BP1, but instead, that the PST repeats can bind to chromatin independently of gammaH2AX.

      Response: We thank the reviewer for spotting this mistake. We carefully checked all references and corrected all wrongly associated ones or used original reports instead of reviews.

      Also, we did re-write some parts of the Introduction as referee #1 also asked for some clarification.

      The data are generally well presented and convincing. The only thing that needs to be added is a quantification of the microscopic analysis (e.g. number of foci per cell, or similar).

      Response: We quantified the foci number in all mutants reported in Figure 2C. These data are now included in the new Figure 2D. Optional: it would be interesting to address the question why plants seem to have two MDC1 orthologues. The longer BCP4 and the shorter BCP3. What is the functional difference between those? Do they perhaps distribute functions that are combined in one protein in vertebrate MDC1 on two different proteins? Response: Thank you for prompting us to address this outstanding question. We now provide evidence supporting that only BCP4 is a functional counterpart of MDC1. We show that a specific region of BCP4 but not BCP3 is able to interact with NBS1 of the MRN complex (see new Figure 6). Also, BCP3 is missing the N-terminal TQxϕ repeats present in BCP4. Although the function of these repeats is unknown at this point, these data together suggest some functional diversification between BCP3 and BCP4. We mention this on page 11, lines 372-374.

      Reviewer #2 (Significance (Required)):

      The strength of the study is the detailed phylogenetic analysis. Also, the biochemistry and cell biology is well done.

      Limitations are the lack of evidence that BCP4 carries out functions in the cell (beyond recognising gammaH2AX) that are carried out by MDC1 in vertebrate cells

      Response: We thank the reviewer for pointing out this important point. To address it we performed pull-down assays with TQxϕ and SQ/DWD regions of BCP4 with NBS1 and found that Arabidopsis NBS1 interacts with the SQ/DWD region, and that this interaction is mediated by FHA+tBRCT of NBS1. Based on Alphafold prediction, we performed further deletion and point mutation analysis of the SQ/DWD region and defined that the binding of NBS1 requires an alpha-helix comprising sequence that is not conserved in BCP3. So, we concluded that a sequence specific of BCP4 (not in BCP3) is capable of recruiting the MRN subunit NBS1.

      At this point we could not demonstrate this in vivo by analyzing NBS1 foci in BCP4 mutant background. Unfortunately, commercial antibodies for plant NBS1 or other subunits of the MRN complex are not available, and to get transgenic plants expressing fluorescent protein tagged NBS1 would require a period much longer than the time for reasonable revisions of a manuscript. Nevertheless, our in vitro interaction data strongly argue for BCP4 having function in binding MRN complex as human MDC1, although the mode of interaction of BCP4 with NBS1 is different from that of human MDC1 and NBS1.

      Please see the new Figure 6 and corresponding description on page 11-12.

      The study is of great interest to readers working on chromatin responses to DNA damage in plants.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Summary The authors set out to find proteins containing BRCT domain to isolate the readers of phosphorylated H2A.X in plants. Using systematic analysis of the BRCT domain proteome, they discovered 21 proteins. Further analysis showed that BCP3 and BCP4 are the ortholog of animal MDC1 and BCP1 is the animal ortholog of PAXIP1. They also extended their work to an evolutionary perspective, finding that BCP1 and BCP4 in plants and PAXIP1 and MDC1 in metazoans evolved independently form a common ancestor. However, this manuscript raises some concerns. Checkout the comments and questions below.

      Major comments: 1) If you think that BCP3 and BCP4 work as a mediator of DDR, can you show us that those mutants have a defect of DDR? The authors only assessed true leaf developing. Leaf developing is affected by not only DNA damage but also other factor. Therefore, authors should show us additional data showing the BCP mutant lines show defective of DNA damage response.

      Response: The “true leaf assay” is a classical assay for testing plant mutants for DNA damage sensitivity (Rosa M, Mittelsten Scheid O Bio. Protoc. 4:e1093. doi: 10.21769/BioProtoc.1093). If DNA damage occurs and is not efficiently repaired, meristematic cells in shoot meristem are arrested and do not divide, hence plants do not produce the first pair of “true” leaves after cotyledons expand. In this assay cotyledons open and grow normally as they are already fully determined and do not undergo any cell division after seed germination.

      In this assay the treated WT seedlings also show a reduction of the number of plants with true leaves as compared with untreated WT (100%). Furthermore, WT and mutant seedlings develop normally and comparably without Zeocin induced DNA damage.

      2) Do you have DNA damage sensitivity data for bcp3 bcp4 double mutants?

      Response: We obtained bcp3bcp4 double mutant and tested it for DNA damage sensitivity. The double mutant is slightly more sensitive than bcp4 single mutant, but not as sensitive as H2A.X mutant. The reason for this is presumably the nature of the bcp3 mutant allele available, with a T-DNA insertion located in the 5’-UTR with some residual expression of BCP3 protein as reported by Vladejic et al., 2022. We did not feel that this would improve the manuscript, so we did not include this data. To obtain a new mutant allele would take time and work beyond the reasonable time required for revision. In addition, since we show that the functional counterpart of MDC1 is BCP4, we did not think that it is relevant to pursue further the characterization of the function of BCP3 in the context of this manuscript.

      3) Some red algae have H2A.X but don't have BCP4 and BCP1 (Figure 4). In this case, how do they read the phosphorylated H2A.X? Can you discuss the point?

      Response: Actually, most red algae do not even have H2A.X. At this point we do not have data that could answer this question and it is difficult to make any prediction about this. Analysis of DDR system in red algae is totally beyond the scope of the current manuscript. See also answer to comment #5.

      4) L307-L312: I thought that the timing of the appearance of SQEF motif in H2A.X differ from the appearance of BCP4 from Figure 4. Why do you say that the evolution of BCP4 and H2A.X coincides?

      Response: we thank the Reviewer for pointing out the need for clarification.

      Histone H2A with a C-terminal SQEF/Y motif is categorized as H2A.X that distinguishes this variant from H2A.Z (not discussed here) and H2A itself. In Archaeplastida many algal species possess either H2A or H2A.X. Only in streptophytes the ancestral gene duplicated leading to neofunctionalization of both H2A and H2A.X and in this case H2A.X form a monophyletic clade. The evolution of BPC1 and 4 are slightly posterior or coincident with this neofunctionalized H2A.X variant, suggesting co-evolution in streptophytes.

      5) Some red algae don't have BCP1, BCP4 and H2A.X. How do they transfer the signal to downstream? Do you have any idea about this?

      Response: To address this interesting question we re-analyzed BRCT domain proteome of the red algae and again could not find any protein containing features of BCP4 present in green algae and land plants or in Opistokont MDC1.

      We did find that red algae without MDC1 do encode MRE11, RAD50 but not NBS1. Also, components of non-homologous end joining DNA repair pathway, Ku70 and Ku80 are conserved in these organisms. So, how some red algae cope with DNA damage remains enigmatic. Similarly unicellular red algae do not have the classical autophagy pathway. This is the result of the very strong genome reduction (Response: Thanks for this comment. We did change title of the manuscript to avoid ambiguity.

      Minor comments: 6) I think you should show us a schematic representation of BAP1 and PAXIP1 to compare both protein features.

      Response: We added schematic presentation of PAXIP1 to Supporting Figure 2B.

      7) L176-L178: Which data support this sentence? Response: The sentence in question: “BCP1 has two tBRCT domains positioned at the N- and C-terminus and a so far unrecognized C-terminal PHD finger which is present in all plant lineages except Brassicaceae (Supporting Figure S1A and S2A).”

      Response: Our data presented on Supporting Figure S1A (schematic presentation of BCP1 protein with indicated PHD finger consensus sequence) and S2A and Source data (alignment of PHD fingers in BCP1 in flowering plants, non-flowering land plants and multicellular green algae) clearly demonstrate the presence of a C-terminal PHD finger in BCP1 except in Brassicaceae. These can also be seen in the full complement of BCP1 sequences that are available in Source data.

      8) L271-L279: There are unreadable characters at "TQx_".

      Response: This very likely appeared during conversion into PDF file. We fixed this now.

      Reviewer #3 (Significance (Required)):

      Significance: General assessment: This study give us an idea how organisms have evolved the upstream system of DDR.

      Advances: This study extend the knowledge of DNA damage response in plants.

      Audience: broad and basic research

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      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)): Evidence reproducibility and clarity The authors report that the human-specific KLF factor KLF7 can induce pluripotency in humans and can improve the reset toward naïve pluripotency when cells are cultured the PXGL medium. KLF7 falls behind KLF4 in reprogramming efficiency but might have a unique role in naïve reset (10-20 fold less efficient in iPSC colony yield). The topic of the study is interesting and adds important insights into the roles of KLF factors along the pluripotency continuum and pinpoints differences between mice and human. There are implications for stem cell engineering and boosting the developmental potency of stem cells (blastoid formation potential, interspecies chimera formation). However, some of the claims as to the unique role of KLF7 are unconvincing in the absence of comparison with other KLF factors, especially the Yamanaka factor KLF4. The flow and coherence of the text can be improved - at times reasoning and motivation of experiments are hard to follow

      Major comments - Why would a pan-pluripotency factor KLF7 which is expressed in both primed and naïve cells more potently trigger the naïve reset than the naïve specific factors KLF4/5/17? Such a comparison could widen the scope and interest of their work.. I would find it interesting if authors would compare the ability of key KLF factors to induce naivety. This is of particular interest as the overexpression of engineered Sox along with KLF4 was reported to improve the quality and developmental potential of PSC in multiple species (MacCarthy et al bioarxiv). Such an analysis could reveal unique features of KLF family members and lead to advanced stem cell models. They actually claim the SK naïve reset does not require naïve medium but the expression of SK alone is sufficient to induce this state. What do the authors think about this claim? Overall I feel the potential role of KLF7 in naïve reset is interesting but underdeveloped.

      We thank the reviewer for the useful comments.

      It has been shown in murine PSCs, that the pluripotency factors Nanog and Oct4 are expressed both at the naive and primed state and their forced expression, in combination with a medium supporting naive pluripotency, efficiently resets primed murine PSCs to naive (Radzisheuskaya A. et al., 2013; Theunissen T. et al., 2011). It is therefore not surprising that a similar regulation might also be conserved in human and that the general pluripotency factor KLF7 is expressed in both states and drives efficient resetting.

      Moreover, we agree that a direct comparison with another KLF factor could improve our work, so thanks to the reviewer’s suggestions, we will generate conventional/primed hPSCs with exogenous KLF4 expression in order to assess the efficiency of chemical resetting compared to hPSCs with overexpression of KLF7.

      Minor comments

      • P3, line 52: "Surprisingly, however, KLF4 is also routinely used to generate conventional human iPSCs." Why is this surprising? KLF4 (and SOX2) are the most potent iPSC factors whilst MYC and OCT4 can be omitted (at least in mouse).

      Thank you for pointing this out. We have rephrased the text accordingly (line 51).

      • It would be nice if the demonstration of pluripotency and quality of KLF7 iPSC go beyond transcriptome profiling and included some further assays common in the field.

      We assessed the quality of our OSK7M iPSCs by performing an EBs differentiation assay (Fig. 3d). We rephrased the text to further highlight this experiment (line 106). Of note, in vivo assays like teratoma formation are not allowed in Italy due to official regulations on animal testing.

      • Fig 1A-B: color coding (of dots) is very confusing- which ones are PSCs and which ones are iPSCs? Another colour palette might fix. What is meant by "interrogating previously published data" (line 67)? Are these public RNA-seq data that were re-analyzed? I

      We will highlight in the figures which cells are PSCs or iPSCs using different colours and shapes.

      We rephrase the text to clarify that available RNA-seq data were reanalysed (line 67).

      • Fig 2b: how were the colony numbers obtained? By morphology, or using live cell staining? So form of staining is recommended colony counting (i.e. TRA-1-60).

      We scored colonies both based on their morphology and after OCT4/NANOG staining. Actually, we observed that the counting based on morphology underestimated the number of iPSC colonies, so it is a more stringent method to score reprogrammed cells.

      • Fig 2e: Also, they say that "[t]hree technical replicates were carried out for all quantitative PCR". Unless I'm mistaken, it seems that only two technical replicates were performed for these qPCR reactions (two dots visible per bar).

      In figure 2e dots refer to two independent experiments. In each experiment we carried out three technical replicates for each sample.

      • Fig 3c: "colture"; change to "culture" (and the title: "bone fide" should be "bona fide")

      Thank you. We amended the typos in the figure and in the text (line 111).

      • For Fig 2/3: since the paper is on KLF4/7, I'm surprised that expression levels of OCT4 and SOX2 were analysed but not KLF4. Given that the main finding was that KLF4 was not upregulated in PSCs, I would be interested to see what the KLF4 levels are like in the iPSCs. RNA-seq analysis/qPCR would be best; but if the authors would like to use other methods, that's fine too.

      This is a good suggestion, we will add to Figure 3b the KLF4 expression levels.

      • Fig 4: The explanatory text is too sparse. Readers should be reminded of the differences between of naïve and primed PSCs and the known roles of KLF4 (this could also be improved in the introduction). List names of naïve media used on top of author names (5iLA, PXGL, EPSCM etc). Why was HENSM by Hanna excluded?

      We will amend the text explaining the main differences between naive and primed PSCs and the role of KLF4.

      We will add PSCs derived in the HENSM medium in the analyses shown in figure 4.

      • Fig 5: KLF7 is classified as a general pluripotency marker, but KLF4/KLF17 are classified as naïve markers. In that case, wouldn't it make more sense to overexpress a naïve specific marker in order to achieve naïve iPSCs at least as a control? What was the motivation here? I think the authors need to provide a more compelling reasoning why only KLF7 was studied or add more data for other KLFs (especially since it seems that the reprogramming efficiency of KLF4 is higher than that of KLF7 for conventional reprogramming (see Fig 2B)...)

      We will perform resetting experiments using KLF4, as suggested, in order to compare the efficiency of KLF7 to a known naive factor.

      o Fig 5B: the text currently says that the cells on the left side of Fig 5B are from Day7; but it says the cells are from Day0 in the actual figure. Which one is it? Also, based on how the text is written, do the cells on the left also contain EOS, or are they the wild-type variety?

      We agree that the text was confusing. Colonies appeared at day 7, but we showed them at day 12, when they were larger and easier to see. We amended the text accordingly. Moreover, the images at day 0 are simply the cell lines at the beginning of the resetting, which also contain EOS, as quantified on the right panels of Fig. 5b.

      o Fig 5c: not all markers in this figure are naïve markers (as stated in the text); would suggest separating the markers and labelling them accordingly AND rewriting the text to reflect that.

      We labelled the markers in the Fig. 5c as suggested by the reviewer and rephrased the text (line 136-137).

      o Life cell reporters for naivety (CD75,SUSD2) could enrich this study.

      We believe that the combination of bulk RNAseq and immunostaining for functional regulators of naive pluripotency (i.e. KLF17 and OCT4 (Lea et al., 2021 Development; Theunissen et al., 2014 Cell Stem Cell) are sufficient to described the acquisition of naive pluripotency.

      • Schemes in 5A/6A could indicate when transgenes were added

      For our chemical resetting experiments we used conventional hiPSCs (KiPS) with stable expression of KLF7 or an EMPTY vector (lines 126-127). We have also added this detail in the figure legends (line 291).

      • Fig 7: the claim regard mouse pluripotency is a little outside of the scope of this paper; would recommend de-emphasizing the claim .

      We will streamline the discussion and put less emphasis on murine PSCs.

      We thank the reviewer for the good suggestion that will be included in the revised manuscript.

      • Similarly, are there features outside the DBD that might suggest a unique activity (IDR, TAD,PTM)? It seems KLF7 generates iPSCs much less efficiently than KLF4. Given the high similarity between their DBDs I wonder why this is so.

      As above, this is an excellent point for discussion that will be added to revised manuscript.

      Reviewer #1 (Significance (Required)): Significance • General assessment: The strength of the study is that the authors provide a potentially new way for the naïve reset in humans. This could improve human stem cell and embryo models. A limitation is that evidence is solely based on molecular (not functional) profiling and the uniqueness of KLF7 versus other KLF's (first and foremost KLF4) was not established. • Advance: Findings on the human-specific role of KLF7 are novel and interesting especially the ability to facilitate the naïve reset. Yet, in the absence of a more systematic comparison with other methods (and KLF factors), the claim that KLF7 is essential for this feat is unconvincing. • Audience: It's of interest to basic researchers in the broader stem cell community and those interested in early embryo development. I work on cellular reprogramming, sequence-structure-function analysis of reprogramming factors and pluripotency.


      Reviewer #2 (Evidence, reproducibility and clarity (Required)): The naïve pluripotency is established in the inner cell mass (ICM) of blastocysts. After implantation, the naïve epiblast becomes primed for lineage specification. Pluripotent stem cells (PSCs) have been successfully derived from early embryos at different stages. In mice, stem cell derivations from ICM yield naïve ESCs. Primed PSCs derived from E5.5-7.5 epiblast are epiblast stem cells (EpiSCs). In humans, stem cell derivations from human embryos have yielded PSCs with features distinct from mouse ESCs and more like EpiSCs. Recently, naïve human PSCs have been directly isolated from pre-implantation epiblast or transformed from primed PSCs. Derivation of naïve hPSCs contributes to studying the molecular events of early lineage specification and accelerates the development of the generation of humanized organs in animal models from naïve hPSCs, opening an exciting avenue for regenerative medicine.

      In this manuscript, the authors found that OSK7M could enable the reprogramming of human primary somatic cells. KLF7 is highly expressed in naive PSCs and its forced expression in conventional hPSCs induces upregulation of naive markers and boosts the efficiency of chemical resetting to naive PSCs, suggesting that KLF7 is a general human pluripotency factor and an inducer of pluripotency. The new findings extend KLF7 function in naïve PSC generation and also provide references for the efficient generation of naive PSCs. The people who focus on studying pluripotency and early embryo development might be interested in and influenced by the findings. The data are in general convincing. However, there are some issues that need to be resolved and improved.

      Major comments:

      1. Line 90: The authors showed that colonies derived from OSKM and OSK7M cocktails could be readily propagated for at least 10 passages. How many passages can OSK7M-iPSCs maintain in vitro prolonged culture?

      And how about the pluripotency and developmental potential of OSK7M-iPSCs for a long-time culture? For example, pluripotency gene expression and teratoma formation.

      We culture OSK7M-iPSCs up to 10 passages without noticing any abnormalities in the morphologies and duplication rate. However, we could extend such cultures for 5-10 more passages (i.e. a total of 2 months from iPSC generation) and perform staining for pluripotency markers or molecular analyses (by qPCR) and EBs differentiation assay to assess their developmental potential.

      In vivo assays like teratoma formation are not allowed in Italy due to official regulations on animal testing.

      1. Overexpression of KLF7 promotes the derivation of naïve PSCs. Are they different from naïve PSCs derived only by chemical resetting? For example, the pluripotency, the in vitro or in vivo developmental potential, and the efficiency of human blastoid generation.

      A key feature of naive PSCs is the potential to differentiate towards the trophoblast lineage in addition to the 3 germ layers. We will perform in vitro differentiation and EB formation assay to gauge the effect of KLF7 on differentiation potential.

      However, establishing a human blastoid generation protocol would be beyond the scope of the current study.

      As the manuscript mentioned, KLF7 is a general human pluripotency factor and an inducer of pluripotency. How does KLF7 knock-out affect the biological characteristics of hESCs? And whether KLF17 KO affects the derivation of naïve PSCs?

      We agree that it would be informative to study the requirement of KLF7 for the maintenance of primed pluripotency and during resetting. We plan to do so either by knockdown or CRISPRi, depending on which technique allows efficient and controllable depletion of KLF7. It might be the case that a straight KO of KLF7 induces the collapse of primed PSCs, making resetting experiments not feasible.

      1. Can naïve PSCs be directly reprogrammed from somatic cells with OSK7M under the PXGL medium? If so, how is the efficiency?

      We believe that studying the role of KLF7 in the context of direct reprogramming of somatic cells to naive pluripotency would go beyond the scope of this manuscript, as it would require substantial work for optimisation and generation of reagents.

      Moreover, we think that both by over-expression and inhibition of KLF7 during resetting, we will be able to investigate its involvement in naive pluripotency acquisition.

      1. Figure 6d: The data showed that in PXGL medium, KiPS (EMPTY) contained about 66% of KLF17+ cells on day 7 and declined to 30% of KLF17+ cells on day 12. Why do KLF17+ cells (naïve PSCs) decline in PXGL medium? Cells overexpressing KLF7 contained about 62% of KLF17+ cells on day 7 and increased to 89% of KLF17+ cells on day 12. Whether KLF7 function at this stage?

      The reviewer raised an intriguing point, concerning the maintenance of naive markers during resetting. Chemical resetting seems to induce transiently >60% of KLF17+/OCT4+ positive cells by day 7, however only a fraction of these cells is stabilised until day 12 (30%). In the presence of KLF7 overexpression, we observed a similar induction at day 7, which is maintained, or increased, up to day 12.

      This would indicate that KLF7 is important for the maintenance of a population of naive cells, rather than only for their induction.

      We will add this important point to the discussion.

      1. Figure 6e: The authors showed transcriptome analysis of KiPS KLF7 cells compared to KiPS16 EMPTY cells in standard culture conditions and found that trophoblast markers were not significantly changed. How is the gene expression during primed to naive transition or TSC differentiation?

      We have already investigated this aspect, showing that at day 12 during primed to naive transition there is a strong induction of TSC markers, which is ablated by KLF7 expression (Fig. 5d). Quantitative immunostaining for GATA3 (TSC marker) confirmed this lack of activation in the presence of KLF7 (Fig. 6c).

      Minor comments:

      1. KLF7 is expressed in both primed and naive PSCs and when overexpressed in conventional PSCs, it enhances chemical resetting to naive PSCs. During primed to naïve transition, how does the KLF7 gene expression pattern change?

      This is a good suggestion, we will analyse the expression patter of KLF7 during resetting.

      1. Line 52: The reference should be added.

      Thank you, we will add the reference.

      1. Line 210-212: The reference should be added.

      Thank you, we will add the reference.

      Reviewer #2 (Significance (Required)): The people who focus on studying pluripotency and early embryo development might be interested in and influenced by the findings. The data are in general convincing. However, there are some issues that need to be resolved and improved.


      Reviewer #3 (Evidence, reproducibility and clarity (Required)): Summary: In this manuscript, the authors found that KLF7 is generally expressed in both prime and naïve human pluripotent stem cells. They showed that KLF7 could replace KLF4 to induce human iPS cells in the microfluidic reprogramming system. The authors then found that overexpression of KLF7 in human prime iPSCs can facilitate the generation of naïve iPS cells. They also showed that KLF7 is a repressor of trophoblast markers. Collectively, these findings indicated that KLF7 is a general pluripotency inducer for human iPS and naïve iPS induction.

      Major comments:

      1. In Figure 2, as the reprogramming efficiency of OSK7M is much lower than that of OSKM, the authors should provide an OSM control to show whether the cells can be reprogrammed without KLF4 and KLF7.

      We have performed the requested experiment (reprogramming with OSM only) as part of a manuscript in preparation. We observed an efficiency of reprogramming significantly lower than OSK7M, yet primary iPS colonies could be obtained.

      We believe that this is due to the expression of KLF4 and KLF7 in human fibroblasts, as shown in Figure 4a.

      1. It will be more convincing to perform a teratoma assay of OSK7M-iPSCs to demonstrate their multilineage differentiation potential.

      In vivo assays like teratoma formation cannot be performed in Italy due to official regulations on animal testing.

      However, we could extend such cultures for 5-10 more passages (i.e. a total of 2 months from iPSC generation) and perform staining for pluripotency markers or molecular analyses (by qPCR) and EBs differentiation assay to assess their multilineage differentiation potential.

      1. Since KLF7 is also expressed in primed human iPS cells, the authors should show the expression level of KLF7 in the established KLF7-iPSC and EMPTY-iPS.

      Good suggestion, we will add it to Figure 3b.

      Minor comments:

      The author claimed that KLF7 is a direct repressor of trophoblast markers, but the data in the manuscript cannot support this conclusion. The author can only claim that KLF7 can inhibit the expression of trophoblast markers.

      We agree with the reviewer, and we believe that there was a misunderstanding. On pages 8-9 line 182-190 we also concluded that KLF7 regulates naive pluripotency markers, rather than trophoblast markers. We will rephrase the text to make it clearer.

      Reviewer #3 (Significance (Required)): KLF family proteins such as KLF4 and KLF17 have been identified as pluripotent inducers. In this study, the authors demonstrated that KLF7 is a novel pluripotent inducer of human IPS and naïve iPS cells, providing new insights into the functions of KLF family proteins in human pluripotency induction.

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      Reply to the reviewers

      Reviewer #1

      The paper by Yammine et al addresses a major problem in peculiarities of genotype to phenotype manifestation in collagen II and chondrodysplasia. It is a lucid and comprehensive study detailing what they see as the fundamental mechanism of Gly1170 Ser mutated Col2a1 gene.

      At the heart of the matter is the debunking of the results from a mouse model generated by liang et al (Plos one 2014) paper in which the authors suggested that the phenotype seen only homozygous mice (heterozygous mice appear normal), was related to ER stress -UPR-apoptosis cascade resulting in the chondrodysplasia. Yammine et al paper uses a different model, a robust human iPSC-based tissue, with a CRISPRed variant show that despite the ability of the variant chondrocytes to deposit a Gly1170Ser-substituted collagen II in both the hetero- and homozygous models, is not accompanied by any substantive UPR. The authors of this current paper also argue that their model system is most closely resemble the human context, where heterozygous individual show pathology.

      We appreciate the Reviewer highlighting the significance of this manuscript addressing a major issue in the field.

      I have sieved all the data related to this topic and have gone back to examine the data and what struck me was the repeated use of the phrase "slow to fold" in the current paper and wondered whether the element of "TIME" is as important in the chondrogenesis of either models and it is this element that generate the difference between the two results? While iPSC-based tissue takes up to 44 days, a female mouse would have had two litters in this time and made many more growth plates. Could it be by "slowing" the chondrogenesis pathway, which is part of the procedure of differentiation of iPS cells into chondrocytes, the ER is not as "stressed" as in mouse development? I would like the authors to reflect and comment and put forward their view given UPR signaling pathways play a crucial role in chondrocytes in phases of high protein synthesis, e.g., during bone development by endochondral ossification (Journal of Bone Metabolism, vol. 24, no. 2, pp. 75-82, 2017).

      The Reviewer here emphasizes a likely benefit of the human model that we had not previously considered, as differentiation and growth in our model are indeed far more similar to humans than the rapid timeline in mice. We also note that the evidence that collagen is slow to fold comes from the gold standard assay in the field for collagen folding rate, a point discussed in greater detail in response to Reviewer 2’s query (see below).

      The literature evidence does indicate that transient UPR signaling is relevant for chondrogenesis. We selected UPR timepoints that do not interface with the differentiation process, but rather the tissue deposition process while chondrocytes are still actively depositing and maintaining the extracellular matrix, to be able to distinguish a physiological transient UPR during differentiation from a potential chronic and possibly pathologic one. We now clarify this point in the manuscript (see text below).

      “These timepoints were selected to reflect an early and a late stage of cartilage maturation, but with both timepoints harvested post-chondrogenesis so as not to interfere with the physiologic transient UPR activation that can be important in that process.”

      This is not withstanding the good argument given by the authors in defending their robust results, namely that the there is no evidence that the hydrophilic triple-helical domain of pro-collagen binds BiP, the main detector of accumulated misfolded proteins. What then do they make out of the immunostaining and qPCR with ER stress related genes in Liang et al paper?? I know that the data is not theirs but a comment on the indisputable data gives the reader a better understanding.

      It is critical to note that the evidence for ER stress that induces the UPR is, at best, exceptionally weak for heterozygotes in the Liang et al paper, and arguably also weak for homozygotes. Liang et al observed, via quantitative PCR, that the mRNA levels of just Chop (which is also a marker of the integrated stress response and not a good readout for UPR activity) and ATF6 (whose RNA-level upregulation is not a standard marker of the UPR) were significantly upregulated in the disease-relevant heterozygous mice – given that other (more valid) UPR markers were not altered, this is not so different from our observation of a lack of UPR in the disease-relevant heterozygotes.

      A somewhat more comprehensive set of UPR markers, including Chop, Xbp1(Total and Spliced), Grp78 (BiP), ATF4, and ATF6, was significantly upregulated only in homozygous mice compared to wild-type. PERK is one of many kinases upstream of ATF4 and Chop that can be activated by a variety of processes (the pathway is part of the integrated stress response, for example). Moreover, transcriptional upregulation of ATF4 (which is actually induced translationally, not transcriptionally) and ATF6 (which is actually induced proteolytically, not transcriptionally) are not normally used to read out UPR activation, so it is not so clear to us that a robust UPR was induced even in homozygotes. Moreover, there was not a substantial increase in Xbp1-S (S = spliced) relative to Xbp1-T (T= total) in the study of homozygous mice, which is the most appropriate measure of UPR activation – rather than change in Xbp1-T and Xbp1-S. The use of mostly non-standard genes to assess UPR induction, the weak upregulation of BiP (2.5-fold), and the unchanged ratio of Xbp1-S to Xbp1-T raise some questions regarding UPR induction even in the homozygotes. Regardless of these homozygote data, as noted above, the evidence for a UPR in heterozygotes is very weak, despite ER stress being the focus of the Liang et al paper.

      With respect to immunostaining, Liang et al observed that tissue from homozygous mice (but not heterozygotes) contained significantly more apoptotic cells. Apoptosis could be a result of chronic, unresolved UPR signaling, but it could also result from any number of other pathways and is certainly not direct evidence for UPR-inducing ER stress. Additionally, for the homozygote apoptosis assay, Liang et al do not note how many mice were analyzed for each genotype, a value they did report for their other assays. While examining multiple sections for each genotype is valuable (they state ≥10), the assessment of biological replicates (additional mice) seems critical to confidently reach a conclusion.

      Although I understand the choice of cell lines for overexpression, the transfection of the HT-1080 cells using wild-type and Gly1170Ser COL2A1encoding plasmids are not a match to the in vivo model (variation of efficiency, etc.) the appearance of BiP even at a lower fold increase does not negate ER stress, as the authors acknowledge but more important is what other paracrine signals which triggers the UPR signally pathway which is not linked to BiP? or an iPS system may lack? Is there anything else not only ATF6α (activating transcription factor 6 alpha), but IRE1α (inositol-requiring enzyme 1 alpha), and PERK (protein kinase RNA-like endoplasmic reticulum kinase).

      Our finding that the UPR is not activated is based on comprehensive RNA-sequencing performed in the physiologically more relevant iPSC-derived chondrocyte, as opposed to the tumor cell line HT-1080. Our interactomic finding that BiP interacts to the same extent with wild-type and Gly1170Ser procollagen-II (in HT-1080 cells) strongly supports our proposal that the reason the UPR is not activated is that BiP fails to recognize unfolded triple-helical domains.

      We note that, although HT-1080 cells are not a perfect match, they are the most accessible option for interactome-based studies. Because there is no MS-grade antibody for collagen-II IP, we need to IP a transfected, tagged collagen. We cannot do this in chondronoids, or in isolated chondrocytes that transfect poorly and rapidly dedifferentiate. Critically, Prockop and co-workers extensively validated HT-1080 cells as a platform for fibrillar collagen biochemical studies in Matrix 1993, 13, 399. Our own lab further characterized their capacity to properly handle fibrillar collagen variants in great molecular detail in ACS Chem Biol 2016, 11__, __1408.

      Since our chondronoid system contains only chondrocyte cells, as is the case in cartilage, the cells can receive paracrine signals from other chondrocytes, but not other cell types. In joints within a whole animal, it is true that paracrine crosstalk occurs between different cell types of different tissues, including inflammatory cells for example. The chondronoid is very useful for elucidating the defects that occur at the chondrocyte-level, without confounding secondary effects. At the chondrocyte-level, Gly1170Ser-substituted procollagen-II does not activate the UPR.

      The Reviewer’s comment regarding the absence of paracrine signals in an iPSC-based system is well-taken, and we added discussion as follows:

      “These observations indicate that the chondrocytes were not raising such stress responses, at least when examined in the absence of paracrine signals from other cell types in the joint.”

      The authors have given us plenty of alternatives that are relevant, and they prepared us for yet another paper on articular cartilage using iPS tissue model which I am looking forward to.

      We are also excited about the upcoming potential of this model system!

      Significance

      I think this paper is publishable and it is important in understanding the mechanism by which mutation in collagen type II affect chondrogenesis and therefore bone formation. This paper will appeal to musculoskeletal scientist especially those who are interested in bone and its pathology. It would be important for the authors to respond to the critique of "TIME" and speed of protein synthesis which create a duress in the ER pathway.

      We greatly appreciate the Reviewer’s comment again on the significance of this work, and their scholarly input which has substantially improved the paper. We hope they will agree that the manuscript is now ready for publication.

      Reviewer #2

      Evidence, reproducibility and clarity

      *System: The investigators have used a human iPSC chondrocyte model system to investigate the biochemistry of the Chondrodysplasia caused by the p.Gly1170Ser mutation in the type II collagen gene (COL2A1). They studied presumably homogeneous chondronoids formed by 3 cell lines they previously reported in which the chondrocytes were either homozygous wild type for the gene, homozygous for the Cas Crispr induced mutation or heterozygous for the two alleles (their refs 42-45). In addition, they utilized cultured HT1080 human fibrosarcoma cells transfected with wild type and mutant Col2A1 to study differences in the interactomes of the two proteins.

      *

      *Analytic Parameters: They investigated the extracellular matrix formed by the three cells using collagen and proteoglycan staining and TEM and the transcriptional responses in chondronoids expressing the wild type and mutant genes.

      *

      *Observations: matrix formation was defective in the two mutation bearing cell populations, reflecting defective fibril formation proportional to the abnormal gene dose. They found increased accumulations of post-translational modifications (hydroxylation, and O-glycosylation) on the mutant collagen extracted from the chondronoids and EM evidence of collagen retention in the ER. They studied the comparative transcriptional profiles in the three phenotypes and failed to find a profound UPR response late in culture and only a mild upregulation of UPR genes in the young cultures. They could not find evidence for activation of the ISR except in the homozygous mutant cells.

      *

      *Using transfected HT-1080 cells (previously shown by these investigators not to express endogenous pro-collagen II but able to synthesize transfected pro-collagen genes) they were able to study the comparative wt and mutant pro-collagen interactomes.

      *

      Conclusions: They conclude that the p.gly1170ser mutation in Col2A1 results in abnormal folding which results in trapping of the protein in the ER and some interaction with cellular elements of the proteostatic response. They concluded that the cellular proteostasis machinery can recognize slow-folding Gly1170Ser through increased interactions with certain ER network components but not in the same fashion that has been described for liver cells producing mutated versions of high volume secreted proteins.

      We appreciate this careful summary of our work.

      *Major comments:

      *

      Their first conclusion, stated in the abstract, "Biochemical characterization reveals that Gly1170Ser procollagen-II is notably slow to fold and secrete." that the mutant polypeptide chain is slower folding than the wild type chain is based on the premise that the longer the chains are in the ER the greater the degree of lysine hydroxylation and O-glycosylation. Although this may be true, they do not provide a reference and I could not find a definitive description of the phenomenon. Their reference 48 only discusses the occurrence of intracellular post-translational modification of the lysines and continuing modification extracellularly but does not relate these phenomena to the rate at which the peptides traverse the cell. I think the reader would benefit from seeing experiments in which the rate of folding and secretion of the wild type and mutant chains are measured and the degree of post-translational modification are compared. Cabral WA et al showed differences in collagen folding and secretion rates in cyclophilin wt, knockouts and heterozygotes osteoblasts and fibroblasts by western blots. (2014) Abnormal Type I Collagen Post-translational Modification and Crosslinking in a Cyclophilin B KO Mouse Model of Recessive Osteogenesis Imperfecta. PLoS Genet 10(6): e1004465. doi:10.1371 / journal.pgen. 1004465). Performing such experiments in their chondronoids would confirm the authors' interpretation that the increased post-translational modification portrayed in their figure 4 reflects slowed folding and secretion related to the mutation.

      We apologize for failing to provide essential background references and information to assess our assay for slow folding/secretion of procollagen. In fact, slow migration on SDS-PAGE is not only a widely used assay for comparing the rate of folding of procollagens, it has also remained the gold standard in the field for the past forty years. The studies cited below are some of the seminal papers in the field linking collagen’s rate of folding with its extent of posttranslational modifications and its electrophoretic mobility. We have now updated our citations accordingly.

      1. Bateman, J.F.; Mascara, T.; Chan, D.; Cole, W.G. “Abnormal type I collagen metabolism by cultured fibroblasts in lethal perinatal osteogenesis imperfecta” Biochem J 1984, 217, 103.
      2. Bonadio, J.; Holbrook, K.A.; Gelinas, R.E.; Jacob, J.; Byers, P.H. “Altered triple helical structure of type I procollagen in lethal perinatal osteogenesis imperfecta” J Biol Chem 1985, 260, 1734.
      3. Bateman, J.F.; Chan, D.; Mascara, T.; Rogers, J.G.; Cole, W.G. “Collagen defects in lethal perinatal osteogenesis imperfecta” Biochem J 1986, 240, 699.
      4. Godfrey, M.; Hollister, D.W. “Type II achondrogenesis-hypochondrogenesis: Identification of abnormal type II collagen” Am J Hum Genet 1988, 43, 904. The basis for this collagen-specific assay of folding rate is that the ER-localized procollagen proline and lysine hydroxylases require monomeric collagen strands as substrates, and cannot accommodate a folded triple helix in their active sites. Thus, accumulation of post-translational modifications on collagen depends on the procollagen triple-helical domain’s residence time as an unfolded monomeric region of the assembling triple-helical trimer within the ER. Some fraction of the hydroxylated lysines are later glycosylated, which slows migration on SDS-PAGE gels. We have now clarified our slow folding conclusion with more precise references and discussion in the manuscript.

      Pulse-chase experiments like those suggested by the Reviewer would indeed be beneficial if they were possible in this system, but they simply are not. Although it might be possible to soak in a radiolabeled amino acid over a short time period, the assay still relies on separating the cell fraction from the secreted fraction. This is possible in monolayer cultures, but in a chondronoid composed of complex cartilage and cells we have no way to do it. One could propose that we extract the chondrocytes and then do the pulse-chase in a monolayer culture, but this unfortunately is also not possible as chondrocytes do not behave well outside the tissue setting and rapidly differentiate into other cell types. Fortunately, the procollagen overmodification assay is a widely used and well-accepted measure of slow folding, and thus addresses the issue.

      I think Figure 4 needs more explanation for the reader. While, as expected, the homozygous mutant band is much slower than the homozygous wild type band, in the heterozygotes the band is intermediate rather than showing a discrete mixture of wild type and mutant proteins, reflecting different degrees of post-translational modification. Is this a function of mixed triple helices with heterogeneous degrees of post-translational modification? It deserves more comment, since the argument relating the degree of post-translational modification to the rate of folding is dependent on this observation. It would also be helpful to show the whole gel with collagen II markers.

      We modified Figure 4 __to show the whole gel (in the SI, see __Fig. S3) and molecular weight markers. It also shows the wild-type collagen-II band. Most of the procollagen produced by the heterozygote is heterotrimeric for the disease-causing substitution (>87% of trimers will contain at least one mutant chain and thus experience delayed folding) and, therefore, the diffuse banding structure is to be expected. Further, we would speculate that in these challenged ER, even the folding of wild-type only trimers is impaired. The Reviewer’s comment suggests there may be some basis for that speculation. We added a note to this effect.

      “The presence of a single broad, slow-migrating band as opposed to distinctive overmodified mutant versus normally modified wild-type strands is due to fact that the vast majority of trimers formed in heterozygotes (>85%) contain at least one Gly1170Ser strand that delays triple-helix folding.”

      Another approach to the question of intracellular accumulation due to a slow rate of folding of the mutant collagen would be to perform pulse chase labeling of the three types of chondronoids with radiolabeled amino acids and sugars and processing the media and lysates with analysis using antibodies specific for the two collagen chain types. Given the authors extensive experience in studying collagen biosynthesis (e.g. Chan et al J. Biochem. Biophys. Methods 36 (1997) 11-29), such a supporting study would firmly establish whether the rate of folding/secretion differs between the wt and the homozygous and heterozygous chondroidinomas. Until the slow folding can be directly demonstrated in a quantitative fashion rather than by monitoring the secondary phenomenon of post-translational modification the hypothesis remains unproven.

      Discussed above in response to the Reviewer’s earlier suggestion of pulse-chase and question regarding the post-translational modification assay, unfortunately the pulse-chase experiment is infeasible. Fortunately, the modification-based assay is already the gold standard in the collagen field.

      Another issue that does not appear to be addressed is the consequence of having misfolded collagen chains in the dilated ER. Liang et al, using mice transgenic for one or two copies of the mutant human gene showed apoptosis in the homozygotes but not in the hets a finding similar to that of Kimura et al using transgenics carrying a different human COL2A1 mutation. Okada et al, using chondrocytes converted from human fibroblasts with clinical collagenopathy (heterozygous), although not the same mutation as in the present study, showed dilated ER and some level of apoptosis in the cultured cells. Hintze et al, examining chondrocytes expressing different mutants associated with different forms of spondyloepiphyseal dysplasia, suggested that the degree of stability of the mutations might determine whether apoptosis occurred, i.e. the thermolabile p.R989C was associated with apoptosis while cells expressing the more thermostable mutants p.275C, P.719C and p.G853E did not reveal any evidence for ongoing apoptosis R989. Is it possible that the smaller size of the homozygous chondronoids reflect fewer cells rather than less matrix (or both) as result of apoptosis? Examination of the chondronoids with reagents for caspase 3 or Tunel staining. One could also measure by Col/DNA ratio in wt, hets and homos. It might also have been useful for these experiments been more quantitative, i.e. by cell sorting rather than by eye. Would ImageJ software been helpful?

      We greatly appreciate this suggestion. We now added results of TUNEL assays performed on sections of the chondronoids (see Fig. 8), including quantification of the results. Notably, we do not observe a significant difference in apoptosis between genotypes at the timepoint considered. This result is also supported by our transcriptional data, where we do not observe upregulation of apoptosis-related pathways, via the UPR or otherwise.

      It is also unclear as to the conformation of chains trapped in the ER. There are many examples in which the natural tendency of misfolded proteins is to aggregate. This is certainly true in the neurodegenerative diseases. While at the magnification used here in the TEM's the ER inclusions appear homogeneous and amorphous, perhaps at higher magnification/resolution a more discrete structure might be seen.

      From collagen-II immunohistochemistry confocal images, the intracellular collagen appears sometimes as aggregated puncta, and in other cases more diffuse and amorphous. Given this heterogeneity, we were not able to readily obtain clear additional structural characterization of the intracellular procollagen-II fraction.

      *While the choice of time points for the transcriptional analysis, i.e. early and late seems well thought out, the lack of a significant response may be due to the timing and it might have been useful to do earlier or later time points or intermediate time points in case the response was transient, particularly since other laboratories have reported UPR activation and abnormalities in the context of the silencing of Xbp1, the spliced form of which is a major driver of at least one arm of the UPR. *

      While our RNA-sequencing results at the specific timepoints we chose cannot rule out a transient activation of the UPR, they do indicate that chronic, unresolved UPR signaling is not the underlying cause of pathology, which is the main point we are making.

      The notion that pro-collagen is largely hydrophilic without the potential for exposure of hydrophobic regions that might engage BiP, thus is not sensitive to BiP sensing, is interesting. Is it possible that the tendency of the mutant polypeptides to form the triple helix which in itself acts as kind of a self chaperoning structure? Looking at the kinetics of assembly inside the cell, see suggestions above, might provide further insight into the process beyond that obtained by looking at the modified state of the lysines.

      We believe this notion is very strongly supported by the interactomic experiment showing that BiP fails to preferentially engage the poorly folding triple-helical variant. There are, however, many other chaperones and folding enzymes that assist collagen folding, including prolyl isomerases and Hsp47. Hence, it is not clear to us that substantial self-chaperoning occurs. Still, the self-chaperoning idea is intriguing, and we will note that prior work does indicate that triple-helical domains of individual procollagen polypeptides are strongly pre-organized for triple-helix formation (for a review, see Annu Rev Biochem 2009, 78, 929). That said, we hesitate to speculate here on the self-chaperoning idea without additional evidence.__

      __Minor comments:

      As I mentioned above, while the transcriptional interactome experiments are computationally sophisticated the cell biology and biochemistry would benefit from more and better quantitation.

      We have included quantitation of the extent of intracellular procollagen accumulation and the extent of apoptotic cells, which we hope helps to address this point.

      The paper is written in a style in which results and discussion are intermingled. Personally I prefer that the introductions are short, the results clearly and briefly presented and the discussion deals with the interpretation and conclusions. I thought that whole paragraphs could have been omitted. e.g. in the introduction *Omit paragraph "The fibrillar.........achondrogenesis type II" Omit paragraph "Conventional and... for example." Omit "Excitingly........in vitro and in vivo (36)." Results: First paragraph repeats last paragraph of introduction and not necessary in one place or the other, condense. *

      We appreciate this feedback and have accordingly edited the manuscript for clarity and brevity, which includes deleting or significantly shortening all the paragraphs indicated by the Reviewer. These improvements are indicated in the track-changes version of the manuscript we resubmitted.

      Figure 2 by eye MGP (Matrix gla protein inhibits vascular calcification of type II collagen) seems highly over-expressed in the homozygous mutants; MGP is supposedly an inhibitor of calcification, does its over-expression here reflect something about the adequacy of the matrix

      Overexpression of MGP could indeed reflect a defect in the matrix of the homozygous variants. It is also likely a reflection of the delayed hypertrophy and maturation observed in the homozygous variants, as matrix calcification is a step in the endochondral ossification process. We did not follow-up on this particular observation, as it is exclusively observed in the less clinically relevant homozygous variant. We added a note to the manuscript to capture the Reviewer’s point about MGP, as below:

      “The upregulation in the homozygous system of Matrix Gla Protein (MGP) (Fig. 2A), which inhibits vascular calcification of the matrix in vivo, further supports the delay in hypertrophy, and could lead to differences in the biomechanical properties of the matrix.”

      Figure 5 is good but can it be confirmed by quantitative biochemistry?

      We have included quantitation of the extent of intracellular procollagen accumulation and the extent of apoptotic cells.

      __ __Did you stain with antibodies to other ER resident chaperones other than calreticulin?

      Yes, we also stained the ER with PDI. However, the chondronoids require extensive optimization for immunostaining and we could obtain much better images using the ER marker for calreticulin, hence our choice of images to present in the manuscript.__

      __Do cells with large amounts of intracellular G1170S die?

      As indicated by the newly included TUNEL data, interestingly, even cells expressing exclusively the Gly1170Ser variant of procollagen-II do not seem to apoptose at a significantly higher rate than wild-type, at least at the timepoint considered. As mentioned above, we added these data as Fig. 8, and added discussion of these results and methodology in the relevant sections of the manuscript.__

      __Does higher magnification EM reveal any structure of the material within the dilated ER?

      We have so far not been able to use EM to obtain higher-resolution insight into intracellular procollagen structures, but we will work on this idea in future studies.__

      __Are there any inflammatory cells in the Chondronoids? To respond to aberrant proteins?

      There should not be any such cells present in the chondronoids, and we indeed do not observe any inflammatory response. As noted in the response to Reviewer 1, we added discussion regarding the absence of paracrine signals in this type of model system, which we do believe has major advantages for biochemical studies like those performed here.__

      __Paragraph

      * "Bypassing the UPR.......often do not" Is discussion not results*

      Corrected, thanks.

      Significance

      The experimental system described here is clearly the wave of the present. Generating human ipSC's of different lineages is now being exploited to study a variety of disorders, to achieve better understanding of pathogenesis at the molecular level to serve as appropriate models for drug development, particularly in the context of high throughput screening. In addition, as in this case, relatively rare autosomal dominant disorders with phenotypes that resemble more common sporadic disease, may allow the development of treatments that are relevant for the sporadic disorder. While it is likely that the osteoarthritis that develops in the carriers of the COL2A1 mutations is a function of the host response to the aberrant mechanics resulting from the defective extra-cellular matrix caused by the mutation, having a pure system in which the primary defect can be corrected and the predisposing matrix deficit reversed, could allow normal reparative processes to mitigate the functional joint disability. While the transgenic mice are useful as a disease model, they represent not only the expression of the primary defect but the host pathophysiologic response to that defect, i.e. in this case how the mouse responds to the defective matrix state and whether those responses add additional pathogenic factors to the disease course. Having a tool in which to relatively assess the pure chondrocyte effect should allow more granular analysis of the primary process.

      We appreciate the Reviewer’s careful and enthusiastic assessment of the significance of our work.__

      __

      Their findings reinforce the notion that involvement of the UPR as well as the other arms of the proteostatic response in chondrocytes expressing a variety of mutant collagens suggests a degree of heterogeneity, perhaps depending on the mutation involved. While I do not believe that their current data prove or rigorously test their proposed hypothesis, i.e. that "perhaps due to the pathologic substitution occurring within a triple-helical domain that lacks hydrophobic character, this ER protein accumulation is not recognized by cellular stress responses, such as the unfolded protein response", it is worth considering.

      We provide that hypothesis as a reasonable explanation for the absence of a UPR, and it is strongly supported by our interactomic studies. Furthermore, neither we nor others have found evidence for BiP binding the triple helical domain of procollagen in any other studies. Still, that hypothesis is not the core point of the paper and we do appreciate the Reviewer’s perspective.

      Given the fact that this is a relatively small field with a variety of observations concerning the role of proteostasis and the UPR in particular which seem to vary depending on the system, i.e. transgenic mice, transfected fibroblasts, the chondroidomas, these observations particularly with additional biochemistry to confirm their notions regarding folding rates etc, represent a useful technical addition to the field and should be interesting for people working on collagen biology, arthritis and protein folding.

      I am not a collagen biologist hence my knowledge of some of the nuances of collagen biology may not be extensive. My own areas of interest include the assembly of multi-peptide proteins (such as immunoglobulins) for secretion; the mechanisms that allow them to exit the cell and the aggregation of misfolded proteins as exemplified by the amyloidoses and other forms of clinically relevant protein aggregation. Hence, I am very familiar with tissue culture, transgenic animals as disease models, studies of protein aggregation, and as a former rheumatologist, osteoarthritis.

      We greatly appreciate the Reviewer providing such valuable and scholarly input from the perspective of a scientist with deep expertise in the secretory pathway and other diseases of protein misfolding, as well as from rheumatology. Specifically from the perspective of expertise in collagen biology/biochemistry, we hope that our detailed explanations of assays that are possible versus not possible with collagen in this system, the additional context for why our assessment of the modification of procollagen is correlated with folding/secretion rate, and the further analyses added to the paper, now make a convincing case that the improved manuscript is of high significance and is ready for publication.

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

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      System: The investigators have used a human iPSC chondrocyte model system to investigate the biochemistry of the Chondrodysplasia caused by the p.Gly1170Ser mutation in the type II collagen gene (COL2A1). They studied presumably homogeneous chondronoids formed by 3 cell lines they previously reported in which the chondrocytes were either homozygous wild type for the gene, homozygous for the Cas Crispr induced mutation or heterozygous for the two alleles (their refs 42-45). In addition, they utilized cultured HT1080 human fibrosarcoma cells transfected with wild type and mutant Col2A1 to study differences in the interactomes of the two proteins.

      Analytic Parameters: They investigated the extracellular matrix formed by the three cells using collagen and proteoglycan staining and TEM and the transcriptional responses in chondronoids expressing the wild type and mutant genes.

      Observations: matrix formation was defective in the two mutation bearing cell populations, reflecting defective fibril formation proportional to the abnormal gene dose. They found increased accumulations of post-translational modifications (hydroxylation, and O-glycosylation) on the mutant collagen extracted from the chondronoids and EM evidence of collagen retention in the ER. They studied the comparative transcriptional profiles in the three phenotypes and failed to find a profound UPR response late in culture and only a mild upregulation of UPR genes in the young cultures. They could not find evidence for activation of the ISR except in the homozygous mutant cells. Using transfected HT-1080 cells (previously shown by these investigators not to express endogenous pro-collagen II but able to synthesize transfected pro-collagen genes) they were able to study the comparative wt and mutant pro-collagen interactomes.

      Conclusions: They conclude that the p.gly1170ser mutation in Col2A1 results in abnormal folding which results in trapping of the protein in the ER and some interaction with cellular elements of the proteostatic response. They concluded that the cellular proteostasis machinery can recognize slow-folding Gly1170Ser through increased interactions with certain ER network components but not in the same fashion that has been described for liver cells producing mutated versions of high volume secreted proteins.

      Major comments:

      Their first conclusion, stated in the abstract, "Biochemical characterization reveals that Gly1170Ser procollagen-II is notably slow to fold and secrete." that the mutant polypeptide chain is slower folding than the wild type chain is based on the premise that the longer the chains are in the ER the greater the degree of lysine hydroxylation and O-glycosylation. Although this may be true, they do not provide a reference and I could not find a definitive description of the phenomenon. Their reference 48 only discusses the occurrence of intracellular post-translational modification of the lysines and continuing modification extracellularly but does not relate these phenomena to the rate at which the peptides traverse the cell. I think the reader would benefit from seeing experiments in which the rate of folding and secretion of the wild type and mutant chains are measured and the degree of post-translational modification are compared. Cabral WA et al showed differences in collagen folding and secretion rates in cyclophilin wt, knockouts and heterozygotes osteoblasts and fibroblasts by western blots. (2014) Abnormal Type I Collagen Post-translational Modification and Crosslinking in a Cyclophilin B KO Mouse Model of Recessive Osteogenesis Imperfecta. PLoS Genet 10(6): e1004465. doi:10.1371 / journal.pgen. 1004465). Performing such experiments in their chondronoids would confirm the authors' interpretation that the increased post-translational modification portrayed in their figure 4 reflects slowed folding and secretion related to the mutation.

      I think Figure 4 needs more explanation for the reader. While, as expected, the homozygous mutant band is much slower than the homozygous wild type band, in the heterozygotes the band is intermediate rather than showing a discrete mixture of wild type and mutant proteins, reflecting different degrees of post-translational modification. Is this a function of mixed triple helices with heterogeneous degrees of post-translational modification? It deserves more comment, since the argument relating the degree of post-translational modification to the rate of folding is dependent on this observation. It would also be helpful to show the whole gel with collagen II markers.

      Another approach to the question of intracellular accumulation due to a slow rate of folding of the mutant collagen would be to perform pulse chase labeling of the three types of chondronoids with radiolabeled amino acids and sugars and processing the media and lysates with analysis using antibodies specific for the two collagen chain types. Given the authors extensive experience in studying collagen biosynthesis (e.g. Chan et al J. Biochem. Biophys. Methods 36 (1997) 11-29), such a supporting study would firmly establish whether the rate of folding/secretion differs between the wt and the homozygous and heterozygous chondroidinomas. Until the slow folding can be directly demonstrated in a quantitative fashion rather than by monitoring the secondary phenomenon of post-translational modification the hypothesis remains unproven.

      Another issue that does not appear to be addressed is the consequence of having misfolded collagen chains in the dilated ER. Liang et al, using mice transgenic for one or two copies of the mutant human gene showed apoptosis in the homozygotes but not in the hets a finding similar to that of Kimura et al using transgenics carrying a different human COL2A1 mutation. Okada et al, using chondrocytes converted from human fibroblasts with clinical collagenopathy (heterozygous), although not the same mutation as in the present study, showed dilated ER and some level of apoptosis in the cultured cells. Hintze et al, examining chondrocytes expressing different mutants associated with different forms of spondyloepiphyseal dysplasia, suggested that the degree of stability of the mutations might determine whether apoptosis occurred, i.e. the thermolabile p.R989C was associated with apoptosis while cells expressing the more thermostable mutants p.275C, P.719C and p.G853E did not reveal any evidence for ongoing apoptosis R989. Is it possible that the smaller size of the homozygous chondronoids reflect fewer cells rather than less matrix (or both) as result of apoptosis? Examination of the chondronoids with reagents for caspase 3 or Tunel staining. One could also measure by Col/DNA ratio in wt, hets and homos. It might also have been useful for these experiments been more quantitative, i.e. by cell sorting rather than by eye. Would ImageJ software been helpful? It is also unclear as to the conformation of chains trapped in the ER. There are many examples in which the natural tendency of misfolded proteins is to aggregate. This is certainly true in the neurodegenerative diseases. While at the magnification used here in the TEM's the ER inclusions appear homogeneous and amorphous, perhaps at higher magnification/resolution a more discrete structure might be seen.

      While the choice of time points for the transcriptional analysis, i.e. early and late seems well thought out, the lack of a significant response may be due to the timing and it might have been useful to do earlier or later time points or intermediate time points in case the response was transient, particularly since other laboratories have reported UPR activation and abnormalities in the context of the silencing of Xbp1, the spliced form of which is a major driver of at least one arm of the UPR. The notion that pro-collagen is largely hydrophilic without the potential for exposure of hydrophobic regions that might engage BiP, thus is not sensitive to BiP sensing, is interesting. Is it possible that the tendency of the mutant polypeptides to form the triple helix which in itself acts as kind of a self chaperoning structure? Looking at the kinetics of assembly inside the cell, see suggestions above, might provide further insight into the process beyond that obtained by looking at the modified state of the lysines.

      Minor comments:

      As I mentioned above, while the transcriptional interactome experiments are computationally sophisticated the cell biology and biochemistry would benefit from more and better quantitation.

      The paper is written in a style in which results and discussion are intermingled. Personally I prefer that the introductions are short, the results clearly and briefly presented and the discussion deals with the interpretation and conclusions. I thought that whole paragraphs could have been omitted. e.g. in the introduction

      Omit paragraph "The fibrillar.........achondrogenesis type II" Omit paragraph "Conventional and... for example." Omit "Excitingly........in vitro and in vivo (36)."

      Results:

      First paragraph repeats last paragraph of introduction and not necessary in one place or the other, condense. Figure 2 by eye MGP (Matrix gla protein inhibits vascular calcification of type II collagen) seems highly over-expressed in the homozygous mutants; MGP is supposedly an inhibitor of calcification, does its over-expression here reflect something about the adequacy of the matrix

      Figure 5 is good but can it be confirmed by quantitative biochemistry?

      Did you stain with antibodies to other ER resident chaperones other than calreticulin?

      Do cells with large amounts of intracellular G1170S die?

      Does higher magnification EM reveal any structure of the material within the dilated ER?

      Are there any inflammatory cells in the Chondronoids? To respond to aberrant proteins?

      Paragraph "Bypassing the UPR.......often do not" Is discussion not results

      Referees cross-commenting

      Are other reviewers concerned about the precise definition of slowed folding rather than utilizing the degree of post-translational modification as a surrogate?

      Significance

      The experimental system described here is clearly the wave of the present. Generating human ipSC's of different lineages is now being exploited to study a variety of disorders, to achieve better understanding of pathogenesis at the molecular level to serve as appropriate models for drug development, particularly in the context of high throughput screening. In addition, as in this case, relatively rare autosomal dominant disorders with phenotypes that resemble more common sporadic disease, may allow the development of treatments that are relevant for the sporadic disorder. While it is likely that the osteoarthritis that develops in the carriers of the COL2A1 mutations is a function of the host response to the aberrant mechanics resulting from the defective extra-cellular matrix caused by the mutation, having a pure system in which the primary defect can be corrected and the predisposing matrix deficit reversed, could allow normal reparative processes to mitigate the functional joint disability. While the transgenic mice are useful as a disease model, they represent not only the expression of the primary defect but the host pathophysiologic response to that defect, i.e. in this case how the mouse responds to the defective matrix state and whether those responses add additional pathogenic factors to the disease course. Having a tool in which to relatively assess the pure chondrocyte effect should allow more granular analysis of the primary process.

      Their findings reinforce the notion that involvement of the UPR as well as the other arms of the proteostatic response in chondrocytes expressing a variety of mutant collagens suggests a degree of heterogeneity, perhaps depending on the mutation involved. While I do not believe that their current data prove or rigorously test their proposed hypothesis, i.e. that "perhaps due to the pathologic substitution occurring within a triple-helical domain that lacks hydrophobic character, this ER protein accumulation is not recognized by cellular stress responses, such as the unfolded protein response", it is worth considering.

      Given the fact that this is a relatively small field with a variety of observations concerning the role of proteostasis and the UPR in particular which seem to vary depending on the system, i.e. transgenic mice, transfected fibroblasts, the chondroidomas, these observations particularly with additional biochemistry to confirm their notions regarding folding rates etc, represent a useful technical addition to the field and should be interesting for people working on collagen biology, arthritis and protein folding.

      I am not a collagen biologist hence my knowledge of some of the nuances of collagen biology may not be extensive. My own areas of interest include the assembly of multi-peptide proteins (such as immunoglobulins) for secretion; the mechanisms that allow them to exit the cell and the aggregation of misfolded proteins as exemplified by the amyloidoses and other forms of clinically relevant protein aggregation. Hence, I am very familiar with tissue culture, transgenic animals as disease models, studies of protein aggregation, and as a former rheumatologist, osteoarthritis.

    1. Refatoração de Código

      A refatoração de código é um processo de melhoria contínua no desenvolvimento de software que envolve a reestruturação do código-fonte sem alterar seu comportamento externo. O objetivo da refatoração é melhorar a legibilidade, a manutenibilidade, a eficiência e a robustez do código, tornando-o mais fácil de entender, modificar e manter ao longo do tempo.

      Melhoria da estrutura:

      A refatoração visa melhorar a estrutura interna do código, tornando-o mais claro, organizado e coeso. Isso pode envolver a divisão de métodos grandes em métodos menores e mais específicos, a eliminação de código duplicado, a simplificação de expressões complexas e a organização de classes e pacotes de forma mais lógica.

      Aprimoramento da legibilidade:

      Um código bem refatorado é mais fácil de ler e entender. Isso é alcançado através da adoção de nomes significativos para variáveis, métodos e classes, da eliminação de comentários desnecessários ou confusos, da formatação consistente do código e da utilização de padrões de projeto que tornam a estrutura do código mais clara.

      Redução da complexidade:

      A refatoração também visa reduzir a complexidade do código, tornando-o mais simples e direto. Isso pode incluir a quebra de métodos ou funções muito complexas em partes menores e mais gerenciáveis, a simplificação de algoritmos complicados e a eliminação de estruturas de controle desnecessariamente complicadas.

      Melhoria da manutenibilidade:

      Um código bem refatorado é mais fácil de manter e atualizar ao longo do tempo. Isso se deve ao fato de que a refatoração torna o código mais modular, com componentes bem definidos e baixo acoplamento, facilitando a identificação e correção de problemas, bem como a adição de novas funcionalidades.

      Aumento da eficiência:

      A refatoração também pode resultar em um código mais eficiente e otimizado. Ao eliminar código redundante, simplificar algoritmos e estruturas de dados, e melhorar o desempenho de operações críticas, a refatoração pode contribuir para a melhoria do desempenho geral do software.

      É importante destacar que a refatoração de código deve ser realizada de forma cuidadosa e incremental, com testes automatizados para garantir que as mudanças não introduzam regressões ou bugs. Além disso, a refatoração é um processo contínuo que deve ser integrado ao ciclo de desenvolvimento de software, sendo uma prática essencial para manter a qualidade e a sustentabilidade do código ao longo do tempo.

    1. , el crite-rio rígido de objetividad del investigador es redefinido como confirma-bilidad de los datos

      Acá se deja más claro por qué acercamientos cualitativos no dejan ser válidos al basarse en conocimiento situado o desde subjetividades.

    2. Tiene como función ilumi-nar conceptualmente aspectos relevantes de los datos o fenómenossociales, y la dirección de sus posibles relaciones, que de otro modo po-drían pasar inadvertidas o no ser comprendidas.

      Da un horizonte de interpretación.

    3. sistema de conceptos, supues-tos, expectativas, creencias y teorías que respaldan e informan la inves-tigación

      ¿Esto haría parte de un marco teórico o conceptual?

    4. actitud

      La idea de situación natural la define Irene Vasilachis como “situaciones, a acciones, a procesos, a acontecimientos reales, concretos, a interacciones espontáneas que, o bien son preexistentes, o bien, en parte tuvieron lugar, o bien se desarrollan durante su presencia en el campo y pueden continuar en su ausencia” (2006, p. 28).

    5. El propósito de este estudio basado en .................... (definirla «tradición» elegida) es .......... (elegir, ya sea: entender; describir; am-pliar, enriquecer, crear teoría; transformar la realidad), las .......... (de-finir el foco o tema central de la investigación), de los ......................(definir las unidades de análisis: individuos, grupos, procesos).En esta investigación el ................... (foco central) será defi-nido como ................ (dar la definición).

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    6. es importante explicitar si los propósitosson descriptivos, teóricos, políticos y prácticos, personales y/o surgende una demanda externa. El primero alude a la necesidad de realizardescripciones densas; el segundo, a la posibilidad de contribuir a laexpansión de la teoría –se replica un estudio en otras unidades deanálisis–, al enriquecimiento conceptual en el interior de la misma, oa la superación y/o creación de nuevos conceptos o teorías. Los terce-ros, los propósitos políticos, aluden a la posibilidad de dar respuestasa problemas que se desea resolver, en diferentes escalas –un grupo so-cial, un aula, un taller, un barrio, una institución–, y a partir de allíelaborar recomendaciones para implementar en prácticas y políticasde acuerdo al nivel, ya sea local o nacional; estos últimos tambiénse denominan propósitos emancipatorios o de empoderamiento.

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    7. La propuesta o proyecto escrito de investigación es undocumento que articula en forma coherente los diferentes elementosque la componen, a través de una argumentación sólida y convincen-te sobre la importancia de llevarla a cabo.

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    8. ralista del investigador al realizar el trabajo de campo, ya que interac-ciona con las personas en su propio ambiente y habla su lenguaje (porlo tanto está lejos del laboratorio o de las aulas, que serían no natura-les), y utiliza una multiplicidad de métodos para registrar datos; seaborda en forma holística las situaciones sociales complejas y es indi-cada para analizar sus procesos y trayectorias.

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    9. los datos produci-dos con este diseño flexible son descriptivos, ricos, son las palabras delos entrevistados, ya sea habladas o escritas, y/o la conducta observa-ble; el análisis de la información es no matemático; se intenta captarreflexivamente el significado de la acción atendiendo a la perspectivadel sujeto o grupo estudiado; la información surge de la actitud natu-

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    10. El diseño estructurado es un plan o protocolo lineal ri-guroso, con una secuencia unidireccional, cuyas fases preestablecidasse suceden en el tiempo y las realizan quizá diferentes personas; estasecuencia se inicia con los propósitos de la investigación hasta arribara la recolección y análisis de los datos.

      Representan una colección de técnicas de análisis y diseño para dar inicio con el propósito de la investigación cualitativa.

      Referencias

      Vasilachis, I. (2006). Estrategias de investigación cualitativa. Biblioteca de educación. Editorial gedisa. Barcelona, España. Tomado de https://investigacionsocial.sociales.uba.ar/wp-content/uploads/sites/103/2013/03/Estrategias-de-la-investigacin-cualitativa-1.pdf

    11. Hay que recordar que las preguntas no son los propósitos de inves-tigación sino que aluden a «qué es lo que se va a estudiar», mientrasque estos últimos apuntan a «por qué se realiza el estudio»

      Preguntas de Investigación: Estas se refieren a qué aspectos específicos se van a estudiar. Son las interrogantes concretas que guían la investigación y buscan comprender, analizar o explorar ciertos fenómenos. Las preguntas de investigación son como brújulas que orientan al investigador hacia los temas relevantes.

      Propósitos de Investigación: Por otro lado, los propósitos de investigación se centran en por qué se realiza el estudio en primer lugar.

    12. es dentro de la teoríafundamentada en donde la construcción de categorías conceptuales y/oteoría es un propósito inherente a ella, o en la etnografía lo es la reali-zación de la «descripción densa».

      Teoría Fundamentada y Etnometodología Se centra en construir teorías a partir de datos recopilados rigurosamente. Busca comprender cómo las personas construyen, prolongan y mantienen sus realidades. La etnometodología estudia la realidad cotidiana y cómo las personas interpretan y actúan en sus mundos sociales.

    13. El concepto deflexibilidad alude a la posibilidad de advertir durante el proceso de in-vestigación situaciones nuevas e inesperadas vinculadas con el temade estudio, que puedan implicar cambios en las preguntas de investi-gación y los propósitos; a la viabilidad de adoptar técnicas novedosasde recolección de datos; y a la factibilidad de elaborar conceptualmentelos datos en forma original durante el proceso de investigación. Esteproceso se desarrolla en forma circular; opuesto, por lo tanto, al derro-tero lineal unidireccional expuesto anteriormente. Por lo tanto, la ideade flexibilidad abarca tanto al diseño en la propuesta escrita, como aldiseño en el proceso de la investigación.

      La idea de flexibilidad abarca tanto la etapa de diseño en la propuesta escrita como el desarrollo continuo del diseño durante todo el proceso de investigación. La flexibilidad implica estar atento a situaciones imprevistas que puedan surgir. Estas pueden estar relacionadas con el tema de estudio y podrían requerir ajustes en las preguntas de investigación o en los objetivos del estudio.

    14. la investigación cualitativa toma a lacomunicación del investigador con el campo y con sus miembros co-mo una parte explícita de la producción de conocimiento. Las subje-tividades del investigador y de los actores implicados son parte delproceso de investigación. Las reflexiones del investigador sobre susacciones, observaciones, sentimientos, impresiones en el campo setransforman en datos, forman parte de la interpretación y son docu-mentadas en diarios de investigación o protocolos de contexto

      La investigación cualitativa reconoce la subjetividad, la comunicación activa y la transformación de reflexiones personales en datos significativos. * Incorpora explícitamente la comunicación entre el investigador y el entorno de estudio. El diálogo, las interacciones y las relaciones con los participantes son fundamentales para comprender los fenómenos. * La percepción personal, las creencias y las experiencias influyen en la interpretación de los datos. * Estas reflexiones enriquecen la comprensión y permiten capturar la complejidad de los contextos estudiados. * Los registros ayudan a rastrear el proceso, validar hallazgos y contextualizar los resultados.

    15. Esta habilidad, denominada sensibilidad teórica oimaginación sociológica, se desarrolla o se aumenta al pensar de modono habitual: estimulando el proceso inductivo, haciendo preguntas alos datos –qué, quién, cómo, dónde, por qué, cuándo–, pensando en si-tuaciones antagónicas o contrarias a las analizadas, incorporando lasdiversas perspectivas de pensamiento, de modo tal que la mente seacomo un prisma en movimiento que capte e irradie luz.

      Lo que debe responder una nueva teoria o conocimiento.

    16. La investigación cualitativa debe ser rigurosa y fiable, por lo tan-to el investigador debe conocer todos los procedimientos necesarios pa-ra producir conocimiento y tener conciencia de su relevancia; al mismotiempo, es deseable que desarrolle su creatividad para incorporar nue-vas técnicas útiles a su estudio.

      El método o camino que se utilizará en la investigación, debe ser de alguna manera un proceso de mixtura, entre lo metodológico, lo ortodoxo y por qué no lo empírico, lo creable, la creatividad propia del investigador puede ser un gran valor de aporte y diferenciador al momento de responder sus preguntas de investigación.

    17. Así, paraCreswell (1998: 85), la etnografía y la fenomenología partirían de uncontexto conceptual elaborado que sería enriquecido y/o replanteadopor los aportes del estudio; en el estudio de caso y estudio biográfico, seda una situación intermedia, ya que si bien pueden partir de una teoría,su propósito es elaborar patrones, taxonomías y modelos; en cambio lateoría fundamentada parte de la necesidad expresa de construir en for-ma inductiva nuevos conceptos relacionados o redefinir los existentesarticulándolos en teorías más generales (

      Realizar etnografia desde una base teorica.

    18. Luego de los propósitos y el contexto conceptual, y siempre mante-niendo el «diálogo e interacción» entre los componentes del diseño, sur-gen o se derivan las preguntas de la investigación. Estas son conside-radas como el «corazón» (Maxwell, 1996) del diseño, indican qué sedesea saber o comprender y a partir de su formulación se conoce la di-rección que tomará la investigación

      En este apartado, (Maxwell, 1996) no pudo ser más claro al calificar a las preguntas de investigación como el corazón o la parte relevante en la construcción de la propuesta de investigación. De ellas dependerá la estructura a desarrollar durante el proceso investigativo. Muchas surgen de escenarios tan interesantes, como conversaciones con colegas, amigos, problemáticas sociales, o simplemente de inquietudes profesionales y opacidades.

    19. a) iniciar el estudiosin ninguna teoría, situación que puede conducir a no poder reconoceraspectos relevantes del fenómeno estudiado, y b) imponer una teoría,descansar en ella, ver la realidad desde una sola perspectiva y tratarde «calzar» los datos en las categorías preconcebidas, o poner «datos re-dondos en categorías cuadradas» (Glaser y Strauss, 1967)

      Errores muy comunes en la investigación en general.

    20. Evidentemente, pueden presentarse uno o varios motivos pararealizar un estudio. Debido a las diferentes tradiciones ya menciona-das en este capítulo, se verá que, por ejemplo, es dentro de la teoríafundamentada en donde la construcción de categorías conceptuales y/oteoría es un propósito inherente a ella, o en la etnografía lo es la reali-zación de la «descripción densa».

      En el orden de ideas de los propósitos o motivos del modelo del diseño de investigación cualitativa, la teoría fundamentada es particularmente fascinante, dado que cuando se trabaja en ella, se permite la validación y conceptos propios del investigador, sin partir de una teoría establecida, si no que se va construyendo durante el análisis y la investigación como tal por parte de quien las realiza.

    21. para Maxwell «es un conjunto de con-ceptos y de relaciones propuestas entre ellas, una estructura queintenta representar o modelar algo sobre el mundo», que «cuenta unahistoria iluminada sobre el fenómeno, que le brinda nuevas ideas, re-velaciones, y amplía su comprensión»

      Concepto de teoria. Para mi tesis

    22. Evidentemente un diseño de investigación y su comunicación enuna propuesta no se logran solamente conociendo metodologías cuali-tativas, sino que son necesarios una sólida formación disciplinar otransdisciplinar y un conocimiento profundo de la problemática a in-vestigar.

      Particularmente conecto con este planteamiento, dado que algunos investigadores novatos o quienes empezamos en estas líneas, preferimos trabajar temáticas que conozcamos y fortalecer la interdisciplinariedad con otros pares investigadores.

    23. El primero alude a la necesidad de realizardescripciones densas; el segundo, a la posibilidad de contribuir a laexpansión de la teoría –se replica un estudio en otras unidades deanálisis–, al enriquecimiento conceptual en el interior de la misma, oa la superación y/o creación de nuevos conceptos o teorías. Los terce-ros, los propósitos políticos, aluden a la posibilidad de dar respuestasa problemas que se desea resolver, en diferentes escalas –un grupo so-cial, un aula, un taller, un barrio, una institución–, y a partir de allíelaborar recomendaciones para implementar en prácticas y políticasde acuerdo al nivel, ya sea local o nacional; estos últimos tambiénse denominan propósitos emancipatorios o de empoderamiento.

      Esto se puede tomar como una rúbrica del trabajo. En el enfoque de para que sirve lo que se esta investigando.

    24. El diseño se convierte en acto o se despliega en el proceso total dela investigación efectivamente desarrollada, y dadas sus particulari-dades tan azarosas, sufre continuas transformaciones que enriquecenfinalmente el estudio final. Por lo tanto, se refiere a la articulación ló-gica de los cinco componentes principales ya mencionados de una pro-puesta de investigación

      El modelo interactivo del diseño en la propuesta de investigación cualitativa, conecta de manera circular, cinco aspectos fundamentales en un proyecto investigativo, girando todos en función de las PREGUNTAS DE INVESTIGACIÓN. En ese orden: 1. Propósitos. 2. Contexto conceptual - fundamentos epistemológicos. 3. Métodos. 4. Criterios de calidad.

    25. del investigador al realizar el trabajo de campo, ya que interac-ciona con las personas en su propio ambiente y habla su lenguaje (porlo tanto está lejos del laboratorio o de las aulas, que serían no natura-les), y utiliza una multiplicidad de métodos para registrar datos; seaborda en forma holística las situaciones sociales complejas y es indi-cada para analizar sus procesos y trayectorias.

      La actitud del investigador ante la fuente de información es supremamente importante. Ademas, se requiere de un estudio previo al contexto donde se va a indagar y recolectar la información.

    26. La investigación cualitativa es un término que alberga en su in-terior una gran variedad de modalidades. Algunas focalizan en: 1) laexperiencia de vida del individuo, en el significado subjetivo de sus ma-nifestaciones, y se basan en los fundamentos teóricos del interaccionis-mo simbólico; constituyen la tradición de la teoría fundamentada y lahistoria de vida, 2) la forma en que se produce el orden social y la cul-tura, utilizando la etnografía, la etnometodología, y el estudio de casos;3) otras se centran en el lenguaje y en la comunicación; y finalmente lacorriente alemana menciona las tradiciones que privilegian 4) las es-tructuras profundas de acción y significado, a través de la hermenéuti-ca

      En este aspecto de la investigación cualitativa, algunos investigadores se sienten más cómodos, (mi caso personal) en especial los que articulan sus trabajos con la documentalización audiovisual. Al utilizar la etnografía, la teoría fundamentada, el estudio de casos y testimoniar o narrar historias, conectan de forma transversal estas variables.

    27. El diseño estructurado es un plan o protocolo lineal ri-guroso, con una secuencia unidireccional, cuyas fases preestablecidasse suceden en el tiempo y las realizan quizá diferentes personas; estasecuencia se inicia con los propósitos de la investigación hasta arribara la recolección y análisis de los datos.

      Los diseños estructurados en algunos casos, se convierten en camisas de fuerza y rigurosos caminos, que debe llevar el investigador. Se trabaja en una sola dirección, partiendo de una hipótesis o teorias ya definidas de antemano.

    28. a) Compromiso con el trabajo de campo: realizarlo en forma res-ponsable, observando y relevando información durante todo el tiemponecesario; registrar las diversas miradas de los participantes que per-mitirán respaldar las conclusiones; redactar notas exactas, completasy precisas, diferenciar entre los datos originales y las propias interpre-taciones, etcétera

      Aquí es importante utilizar las herramientas de bolsillo que hemos visto durante este semestre para ir creando un repositorio o memoria viva del proceso.

    29. Además, los datos produci-dos con este diseño flexible son descriptivos, ricos, son las palabras delos entrevistados, ya sea habladas o escritas, y/o la conducta observa-ble; el análisis de la información es no matemático; se intenta captarreflexivamente el significado de la acción atendiendo a la perspectivadel sujeto o grupo estudiado

      En este aparte encontramos las características de los DATOS, dentro del diseño flexible. PREGUNTA: ¿se puede ampliar en los métodos para registrar los datos?

    30. Se vincula este tipo de diseño a la investigación cualitativa induc-tiva que desea crear conceptos, hipótesis, modelos y/o teoría desde losdatos empíricos. Pero también es posible utilizar este diseño en inves-tigaciones cuantitativas que, utilizando datos secundarios –obtenidosen forma rigurosa–, se propongan crear teoría y nuevos conceptos, ana-lizándolos en forma libre e inductiva (Glaser y Strauss, 1967: 185; Gla-ser, 1978: 6)

      Resalto otra característica: la creación de conceptos, hipótesis, modelos, teorías desde datos empíricos., con el fin de crear teoría y nuevo conceptos. PREGUNTA: ¿este modelo hace parte o se nutre de la teoría fundamentada?

    31. investigación se presenta la posi-bilidad de modificarlos o superarlos. Desde el inicio de la investigaciónla recolección de datos, el análisis, la interpretación, la teoría, se danconjuntamente, y esta ida y vuelta entre los datos y la teorización per-mite generar interactivamente conocimiento fundado en los datos.

      La clave es el diálogo interactivo entre los datos.

    32. Generalmente se ha asociado este diseño a los estudios socialescuantitativos interesados en la verificación. Si simplificamos los ras-gos diversos de estos estudios, podemos afirmar que se inician conhipótesis definidas de antemano o con conceptos rigurosamente opera-cionalizados –indicadores, variables–; además, en las categorías pre-concebidas de estas variables, se clasifican unidades de análisis perte-necientes a muestras probabilísticas, y estas categorías cumplen conlos criterios de exhaustividad, mutua exclusión y relevancia; si las uni-dades de análisis son individuos, cada persona es interrogada con elmismo tipo de preguntas preelaboradas por el investigador en cuestio-narios pautados. El objetivo es garantizar la comparabilidad de los da-tos en el interior de cada categoría, y posteriormente obtener, por infe-rencia estadística, el conocimiento de las características medibles entodo el universo de unidades de análisis de referencia. Los datos sonnúmeros, ya sea porque se trata con variables cuantitativas o con lasfrecuencias de variables de diversos niveles de medición; además, suanálisis es matemático: porcentajes, modo, mediana, media, correlacio-nes, regresiones y/o asociaciones, entre otros

      CARACTERÍSTICAS DEL DISEÑO ESTRUCTURADO - Cuantitativos - Inician con hipótesis - Se entrecruza con conceptos rigurosos: indicadores, variables, unidades de análisis - Su desarrollo es en forma lineal - Las categorías cumplen con criterios de exhaustividad, exclusión y relevancia - Los datos son numéricos - El objetivo es garantizar la comparabilidad de los datos en el interior de cada categoría, y obtener por inferencia estadísitica el conocimiento de las unidades de análisis de referencia.

    1. y se define generalmente de la siguiente manera.

      ¿De qué manera?

      Si usas "siguiente" es porque está ahí nomás, pero lo que sigue es información sobre ventajas y desventajas. Podría escribirse la ecuación justo después de "y se define de la siguiente manera" o se podría quitar lo subrayado y escribir antes de la ecuación algo así como "La siguiente ecuación define el error porcentual absoluto medio:"

    2. La ecuación (5.28)

      Así está muy bien. Como todo el estilo de redacción debe ser homogéneo, tendrías que cambiar todo lo anterior a algo como aquí, o escribir aquí "La Ecuación 5.28 es una generalización de la Ecuación 5.17"

    3. as ecuacio

      No debe decir "Las ecuaciones Ecuación 5.25 a Ecuación 5.27" ... esto se observa en varias líneas de tu tesis y seguramente tiene que ver en con el estilo elegido para la escritura en LaTex o cómo declaraste la forma de hacer referencias. Lo ideal es que al hacer la referencia sólo aparezca el número, aunque de manera manual escribas si se trata de una ecuación, una figura, un teorema etcétera. al referise a algo, digamos, una ecuación, debe escribirse "la ecuación 4.8 " ... en tu redacción habría que hacer que Ecuación, Figura... etcétera comience con minúscula en la mayoría de los casos. No tengo problema si queda así como está pero hay que cuidar que no aparezca dos veces figura Figura, o ecuaciones Ecuación...etcétera.

      Para esta parte, se podría escribir algo así como: Al analizar la ecuación 5.25 a la ecuación 5.27, queda la impresión de que...

      También podrías adecuarla de tal modo que no aparezca ecuaciones Ecuación.

    1. AbstractComputational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDSTB). As specific computational tools are often required for a given disease, developing a disease specific web portal is highly desirable. This paper emphasises on the development of the customised web portal for COVID-19 infection and is referred to as MPDSCOVID-19. Expectedly, the MPDS suites of programs have modules which are essentially independent of a given disease, whereas some modules are specific to a particular disease. In the MPDSCOVID-19 portal, there are modules which are specific to COVID-19, and these are clubbed in SARS-COV-2 disease library. Further, the new additions and/or significant improvements were made to the disease independent modules, besides the addition of tools from galaxy toolshed. This manuscript provides a latest update on the disease independent modules of MPDS after almost 6 years, as well as provide the contemporary information and tool-shed necessary to engage in the drug discovery research of COVID-19. The disease independent modules include file format converter and descriptor calculation under the data processing module; QSAR, pharmacophore, scaffold analysis, active site analysis, docking, screening, drug repurposing tool, virtual screening, visualisation, sequence alignment, phylogenetic analysis under the data analysis module; and various machine learning packages, algorithms and in-house developed machine learning antiviral prediction model are available. The MPDS suite of programs are expected to bring a paradigm shift in computational drug discovery, especially in the academic community, guided through a transparent and open innovation approach. The MPDSCOVID-19 can be accessed at http://mpds.neist.res.in:8085.

      This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.114), and has published the reviews under the same license. These are as follows.

      Reviewer 1. Prashanth N Suravajhala

      Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is? Yes. The authors could describe Minimum Information about bioinformatics investigation (MIABI) guidelines. Is the source code available, and has an appropriate Open Source Initiative license been assigned to the code? github and Zenodo, yes!

      I tested git, forked it and as I didn't test the graphical version, ensured all python libraries are working! Is the documentation provided clear and user friendly? Yes. Yes, a white paper could be more friendly! Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level? Yes. yes with README version! Have any claims of performance been sufficiently tested and compared to other commonly-used packages? Yes, as described by the authors Are there (ideally real world) examples demonstrating use of the software? Yes. The Molecular Property Dynamic Suite (MPDS) is a welcome initiative which would serve chemical space for research community. While the authors aimed to deploy it in Galaxy, there is no Galaxy reference cited in first few introductory lines. A strong rationale on Galaxy-MPDS connect could be a value addition The port 8085/8080 are ephemeral and it would be nice if the authors deploy it on a more permanent base An absolute strength for the suite is availability of source code so that end-users can fine tune and reinstantiate the codes. In the architecture, could the end user have a chance to deploy biopython modules for drug discovery/modeling

      In Page 4, the authors can define what are the tools precisely used in MPDS 2.3 section: The PPI is not abbreviated as first use The results are exploited well for disease dependent/independent use. However, the major challenge for ligand use/preparation is the use of ncRNAs. Could MPDS provide such instances where ncRNAs could be used fpr targeted ligands? L28 in section 4.1: Pluralis for features ( as one of is used) Also a word or two on aadhar card for perhaps naive users may be mentioned and it may be italicized as it may be a domestic word. Does MPDS suite augur well for Anvaya that Government of India launched, or Tavexa or Taverna? A word to two on local setting up of cloud instance may be a nice addition

      Scores on a scale of 0-5 with 5 being the best

      Language: 4 Novelty: 4.5 Brevity: 4 Scope and relevance: 4 Language/Brevity checks: Page 9 L6: fulfill misspelt webserver are two words, IMHO

      Page 10: CADD which IS available

      Tabl S2/S4: from THE coronavirdiae space between anticoronavirusdrugs

      Figure S3: remove OF (identifying OF existing) Supporting information may be corrected High resolution Figures esp GA, Figures 2-4 may be inserted

      Reviewer 2. Abdul Majeed

      Is the language of sufficient quality? Yes. Some changes are needed to make the writing more scientific. Is the code executable? Unable to test Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined? Unable to test

      Additional comments: In this paper, the authors introduced a Molecular Property Diagnostic Suite (MPDS), which is a Galaxy-based web portal that was conceived and developed as an open-source disease-specific web portal. MPDS is a customized web portal developed for COVID-19, which is a one-stop solution for drug discovery research. I read the article; it is well-written and well-presented. The enclosed contents can be very useful for researchers working in this field (e.g., COVID-19 systems development). However, I propose some comments/concerns to the current version that need correction during the revision. 1- In the abstract, please provide the technical description of the method’s working. Also, please mention the entities which can benefit from the system. 2- The introduction section doesn’t present the challenges/problems of the existing tools. Please discuss the challenges of the previous such tools and how are they addressed through this new system. 3- I could not find the concrete details of data modalities supported in the system. The authors are advised to include such details. 4- The authors mentioned the use of ML, but I couldn’t find any potential usage of ML models. Please add such analysis during the revision. 5- Also, please add some performance results like time complexity, storage, I/O cost, etc. 6- One comprehensive diagram should be included to better illustrate the working of the proposed tool. 7- Please add limitations of the proposed tool in the revised work. 8- Please add the potential implications of this tool in the context of current/future pandemics.

      Re-review: I have carefully checked the revised work and the author's responses. The authors have made the desired modifications. I have no major concerns on this paper. In the previous review round, Comment #: 3 has not been properly responded by the authors. By data modality, I meant tabular data, graph data, audio data, video data, etc. Authors should add this aspect clearly in the paper about each data modality processed in their system. In Figure 4, some contents (e.g., protein information, PPI interaction, etc.) are unreadable. The abbreviations are not consistently written in terms of small and capital letters. In the paper, the authors are advised to clearly describe the purpose of this tool, who will benefit and in what capacity, why these kinds of tools are needed, etc. I suggest adding such information in abstract to clearly convey the message to readers. In the title, please recheck one word, Open Access or Open Source. The journals are open access while the software are usually open source .

      Reviewer 3. Agastya P Bhati

      Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is? Yes. As noted in my comments, it would be beneficial to clarify what new capabilities are provided by this new portal over and above what is already available currently. Is the source code available, and has an appropriate Open Source Initiative license been assigned to the code? No. There is a github repository (https://github.com/gnsastry/MPDS-18Compound_Library), however, I am unable to access it currently. As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code? Yes. A github repository provides such capabilities. However, it is inaccessible currently. Is the code executable? Unable to test Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined? Unable to test Have any claims of performance been sufficiently tested and compared to other commonly-used packages? Is automated testing used or are there manual steps described so that the functionality of the software can be verified? No Additional comments: Molecular Property Diagnostic Suite for COVID-19 (MPDSCOVID19) is an open-source disease specific web portal aiming to provide a collection of all tools and databases relevant for COVID-19 that are available online along with a few in-house scripts at a single portal. It is built upon another platform called "Galaxy" that provides similar services for data intensive biomedical research. MPDSCOVID19 is in continuation to two other similar disease-specific portals that this group has published earlier - for Tuberculosis and Diabetes mellitus. Overall, MPDSCOVID19 is an interesting and useful resource that could be helpful for biomedical community in conducting COVID-19 related research. It brings together all the databases and relevant tools that may make a researcher's life easier as exemplified through the various case studies included.

      I recommend publishing this article after the following revisions noted. Please note that any mention of page numbers below is referring to the reviewer PDF version.

      Major revisions:

      (1) One main issue in this manuscript is the lack of a clear description of the "new" capabilities provided by MPDSCOVID19 over and above what Galaxy provides. I think a clear distinction between the capabilities/features of Galaxy and MPDSCOVID19 would help improve the manuscript substantially and help readers better understand the capabilities of this new COVID-19 portal.

      Further, a description of the additions in the new portal over the earlier TB and Diabetes portals is mentioned on page 7. However, I think more details on such advancements/additions would be beneficial. It could be in the form of a table.

      (2) It is mentioned that a major advancement in this new portal is the inclusion of ML/AI models/approaches, however no details have been provided. It would be beneficial to briefly describe what ML based capabilities are included in MPDS and how they can be used by any general user. An additional case study demonstrating the same would be helpful.

      (3) MPDS portal provides a collection of tools and databases for COVID-19. However, such resources are ever-growing and hence constant updating of the portal's capabilities/resources would be a necessary requirement for its sustainability. There is no mention of any such plans. Do authors have a modus operandi for the same? Have there been further releases of the previous MPDS portals for TB and Diabetes that may be relevant here?

      (4) Page 6 - lines 3-4: I suggest replacing "are going to witness" with "are witnessing". There are several recent advancements in applying ML/AI based approaches to improve different aspects of drug discovery. I recommend including a few references here to this effect. Below are some relevant examples:

      (a) 10.1021/acs.jcim.0c00915 (b) 10.1021/acs.jcim.1c00851 (c) 10.1038/s41598-023-28785-9 (d) 10.1098/rsfs.2021.0018 (e) 10.1145/3472456.3473524 (f) 10.1145/3468267.3470573

      (5) Page 7 - line 8: I am assuming that the terms like "updates", "additions", etc., used in this paragraph are comparing MPDS with its older versions. If so, it would be beneficial to clarify this explicitly. In addition, I suggest that the authors include a brief literature survey to describe what other tools and/or webservers are available already and how MPDS compares with them. This has not been done so far.

      (6) The github repository is currently inaccessible publicly. This needs rectification.

      Minor revisions:

      (1) Page 4: Before introducing MPDSCOVID19 it makes sense to briefly describe Galaxy and its main features. For instance moving forward lines 19-20 (page 4) and lines 3-6 (page 5) to line 12 (page 4).

      (2) Page 5 - line 22: I suggest that authors mention the total number of databases/servers that are covered by MPDSCOVID19 as of now. From Table S1, it appears that there are 15 currently (items 5 and 7 are repeated so the 13 seems the wrong total - needs rectification).

      (3) Page 5 - line 30: It would make sense to specify details of the MPDS local server. For instance, how many cores/GPUs are available and what are their hardware architectures? Also, it would be beneficial for the users to know if it is possible to use MPDS tools on their own or public infrastructures for large scale implementations. I suggest authors comment on this aspect too.

      (4) Page 6 - lines 16-19: The sentence "Galaxy platform.......extend the availability." needs some rephrasing. It is too long and the hard to comprehend.

      (5) Page 7 - line 18: I don't understand the word "colloids". Please clarify.

      (6) Page 8 - line 30: "section 2.3" is referred to but I don't see any section numbering the PDF provided. This needs rectification.

      Re-review: I am satisfied with the changes made to the manuscript and recommend publishing it in its current form if all other reviewers are happy with that.

    1. direito de regresso

      Ação movimentada por quem indenizou o prejudicado contra o agente que causou o prejuízo de forma dolosa ou culposa. NATUREZA CÍVIL.

    2. interoperabilidade

      refere-se aos padrões, protocolos, tecnologias e mecanismos que permitem que os dados fluam entre diversos sistemas com o mínimo de intervenção humana

    1. Author Response

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

      Reviewer #1 (Recommendations For The Authors):

      I only have a few minor suggestions:

      Abstract: I really liked the conclusion (that IM and VWM are two temporal extremes of the same process) as articulated in lines 557--563. (It is always satisfying when the distinction between two things that seem fundamentally different vanishes). If something like this but shorter could be included in the Abstract, it would highlight the novel aspects of the results a little more, I think.

      Thank you for this comment. We have added the following to the abstract:

      “A key conclusion is that differences in capacity classically thought to distinguish IM and VWM are in fact contingent upon a single resource-limited WM store.”

      L 216: There's an orphan parenthesis in "(justifying the use".

      Fixed.

      L 273: "One surprising result was the observed set size effect in the 0 ms delay condition". In this paragraph, it might be a good idea to remind the reader of the difference between the simultaneous and zero-delay conditions. If I got it right, the results differ between these conditions because it takes some amount of processing time to interpret the cue and free the resources associated with the irrelevant stimuli. Recalling that fact would make this paragraph easier to digest.

      That is correct. However, at this point in the text, we have not yet fitted the DyNR model to the data. Therefore, we believe that introducing cue processing and resource reallocation as concepts that differentiate between those two conditions would disrupt the flow of this paragraph. We address these points soon after, in a paragraph starting on line 341.

      Figures 3, 5: The labels at the bottom of each column in A would be more clear if placed at the top of each column instead. That way, the x-axis for the plots in A could be labeled appropriately, as "Error in orientation estimate" or something to that effect.

      We edited both figures, now Figure 4 and Figure 6, as suggested.

      L 379: It should be "(see Eq 6)", I believe.

      That is correct, line 379 (currently line 391) should read ‘Eq 6’. Fixed.

      L 379--385: I was a bit mystified as to why the scaled diffusion rate produced a worse fit than a constant rate. I imagine the scaled version was set to something like

      sigma^2_diff_scaled = sigma^2_base + K*(N-1)

      where N is the set size and sigma^2_base and K are parameters. If this model produced a similar fit as with a constant diffusion rate, the AIC would penalize it because of the extra parameter. But why would the fit be worse (i.e., not match the pattern of variability)? Shouldn't the fitter just find that the K=0 solution is the best? Not a big deal; the Nelder-Mead solutions can wobble when that many parameters are involved, but if there's a simple explanation it might be worth commenting on.

      The scaled diffusion was implemented by extending Eq 6 in the following way:

      σ(t)2 = (t-toffset) * σ̇ 2diff * N

      where N is set size. Therefore, the scaling was not associated with a free parameter that could become 0 if set size did not affect diffusion rate, but variability rather mandatory increased with set size. We now clarify this in the text:

      “The second variant was identical to the proposed model, except that we replaced the constant diffusion rate with a set size scaled diffusion rate by multiplying the right side of Eq 6 by N.“

      Figure 4 is not mentioned in the main text. Maybe the end of L 398 would be a good place to point to it. The paragraph at L 443-455 would also benefit from a couple of references to it.

      Thank you for this suggestion. Figure 4 (now Figure 5) was previously mentioned on line 449 (previously line 437), but now we have included it on line 410 (previously line 398), within the paragraph spanning lines 455-467 (previously 443-455), and also on line 136 where we first discuss masking effects.

      L 500: Figure S7 is mentioned before Figures S5 and S6. Quite trivial, I know....

      Thank you for this comment. There was no specific reason for Figure S7 to appear after S5 & S6, so we simply swapped their order to be consistent with how they are referred to in the manuscript (i.e., S7 became S5, S5 became S6, and S6 became S7).

      Reviewer #2 (Recommendations For The Authors):

      (1) One potential weakness is that the model assumes sensory information is veridical. However, this isn't likely the case. Acknowledging noise in sensory representations could affect the model interpretation in a couple of different ways. First, neurophysiological recordings have shown normalization affects sensory representations, even when a stimulus is still present on the screen. The DyNR model partially addresses this concern because reports are drawn from working memory, which is normalized. However, if sensory representations were also normalized, then it may improve the model variant where subjects draw directly from sensory representations (an alternative model that is currently described but discarded).

      Thank you for this suggestion. We can consider two potential mechanisms through which divisive normalization might be incorporated into sensory processing within the DyNR model.

      The first possibility involves assuming that normalization is pre-attentive. In this scenario, the sensory activity of each object would be rescaled at the lowest level of sensory processing, occurring before the allocation of attentional or VWM resources. One strong prediction of such an implementation is that recall error in the simultaneous cue condition (Experiment 1) should vary with set size. However, this prediction is inconsistent with the observed data, which failed to show a significant difference between set sizes, and is more closely aligned with the hypothesis of no-difference (F(2,18) = 1.26, p = .3, η2 = .04, BF10 = 0.47). On that basis, we anticipate that introducing normalization as a pre-attentive mechanism would impair the model fit.

      An alternative scenario is to consider normalization as post-attentive. In the simultaneous cueing condition, only one item is attended (i.e., the cued one), regardless of the displayed set size. Here, we would expect normalized activity for a single item, regardless of the number of presented objects, which would then be integrated into VWM. This expanded DyNR model with post-attentive normalization would make exactly the same predictions as the proposed DyNR for recall fidelity, so distinguishing between these models would not be possible based on working memory experiments.

      To acknowledge the possibility that sensory signals could undergo divisive normalization and to motivate future research, we have added the following to our manuscript:

      “As well as being implicated in higher cognitive processes including VWM (Buschman et al, 2011; Sprague et al., 2014), divisive normalization has been shown to be widespread in basic sensory processing (Bonin et al., 2005; Busse et al., 2009; Ni et al., 2017). The DyNR model presently incorporates the former but not the latter type of normalization. While the data observed in our experiments do not provide evidence for normalization of sensory signals (note comparable recall errors across set size in the simultaneous cue condition of Experiment 1), this may be because sensory suppressive effects are localized and our stimuli were relatively widely separated in the visual field: future research could explore the consequences of sensory normalization for recall from VWM using, e.g., centre-surround stimuli (Bloem et al., 2018).”

      Bloem, I. M., Watanabe, Y. L., Kibbe, M. M., & Ling, S. (2018). Visual Memories Bypass Normalization. Psychological Science, 29(5), 845–856. https://doi.org/10.1177/0956797617747091

      Bonin, V., Mante, V., & Carandini, M. (2005). The Suppressive Field of Neurons in Lateral Geniculate Nucleus. The Journal of Neuroscience, 25(47), 10844–10856. https://doi.org/10.1523/JNEUROSCI.3562-05.2005

      Buschman, T. J., Siegel, M., Roy, J. E., & Miller, E. K. (2011). Neural substrates of cognitive capacity limitations. Proceedings of the National Academy of Sciences, 108(27), 11252–11255. https://doi.org/10.1073/pnas.1104666108

      Busse, L., Wade, A. R., & Carandini, M. (2009). Representation of Concurrent Stimuli by Population Activity in Visual Cortex. Neuron, 64(6), 931–942. https://doi.org/10.1016/j.neuron.2009.11.004

      Ni, A. M., & Maunsell, J. H. R. (2017). Spatially tuned normalization explains attention modulation variance within neurons. Journal of Neurophysiology, 118(3), 1903–1913. https://doi.org/10.1152/jn.00218.2017

      Sprague, T. C., Ester, E. F., & Serences, J. T. (2014). Reconstructions of Information in Visual Spatial Working Memory Degrade with Memory Load. Current Biology, 24(18), 2174–2180. https://doi.org/10.1016/j.cub.2014.07.066

      Second, visual adaptation predicts sensory information should decrease over time. This would predict that for long stimulus presentation times, the error would increase. Indeed, this seems to be reflected in Figure 5B. This effect is not captured by the DyNR model.

      Indeed, neural responses in the visual cortex have been observed to quickly adapt during stimulus presentation, showing reduced responses to prolonged stimuli after an initial transient (Groen et al., 2022; Sawamura et al., 2006; Zhou et al., 2019). This adaptation typically manifests as 1) reduced activity towards the end of stimulus presentation and 2) a faster decay towards baseline activity after stimulus offset.

      In the DyNR model, we use an idealized solution in which we convolve the presented visual signal with a response function (i.e., temporal filter). At the longest presentation durations, in DyNR, the sensory signal plateaus and remains stable until stimulus offset. Because our psychophysical data does not allow us to identify the exact neural coding scheme that underlies the sensory signal, we tend to favour this simple implementation, which is broadly consistent with some previous attempts to model temporal dynamics in sensory responses (e.g., Carandini and Heeger, 1994). However, we agree with the reviewer that some adaptation of the sensory signal with prolonged presentation would also be consistent with our data.

      We have added the following to the manuscript:

      “In Experiment 2, the longest presentation duration shows an upward trend in error at set sizes 4 and 10. While this falls within the range of measurement error, it is also possible that this is a meaningful pattern arising from visual adaptation of the sensory signal, whereby neural populations reduce their activity after prolonged stimulation. This would mean less residual sensory signal would be available after the cue to supplement VWM activity, predicting a decline in fidelity at higher set sizes. Visual adaptation has previously been successfully accounted for by a type of delayed normalization model in which the sensory signal undergoes a series of linear and nonlinear transformations (Zhou et al., 2019). Such a model could in future be incorporated into DyNR and validated against psychophysical and neural data.”

      Carandini, M., & Heeger, D. J. (1994). Summation and division by neurons in primate visual cortex. Science, 264(5163), 1333–1336. https://doi.org/10.1126/science.8191289

      Groen, I. I. A., Piantoni, G., Montenegro, S., Flinker, A., Devore, S., Devinsky, O., Doyle, W., Dugan, P., Friedman, D., Ramsey, N. F., Petridou, N., & Winawer, J. (2022). Temporal Dynamics of Neural Responses in Human Visual Cortex. The Journal of Neuroscience, 42(40), 7562–7580. https://doi.org/10.1523/JNEUROSCI.1812-21.2022

      Sawamura, H., Orban, G. A., & Vogels, R. (2006). Selectivity of Neuronal Adaptation Does Not Match Response Selectivity: A Single-Cell Study of the fMRI Adaptation Paradigm. Neuron, 49(2), 307–318. https://doi.org/10.1016/j.neuron.2005.11.028

      Zhou, J., Benson, N. C., Kay, K., & Winawer, J. (2019). Predicting neuronal dynamics with a delayed gain control model. PLOS Computational Biology, 15(11), e1007484. https://doi.org/10.1371/journal.pcbi.1007484

      (2) A second potential weakness is that, in Experiment 1, the authors briefly change the sensory stimulus at the end of the delay (a 'phase shift', Fig. 6A). I believe this is intended to act as a mask. However, I would expect that, in the DyNR model, this should be modeled as a new sensory input (in Experiment 2, 50 ms is plenty of time for the subjects to process the stimuli). One might expect this change to disrupt sensory and memory representations in a very characteristic manner. This seems to make a strong testable hypothesis. Did the authors find evidence for interference from the phase shift?

      The phase shift was implemented with the intention of reducing retinal after-effects, essentially acting as a mask for retinal information only; crucially the orientation of the stimulus is unchanged by the phase shift, so from the perspective of the DyNR model, it transmits the same orientation information to working memory as the original stimulus.

      If our objective were to model sensory input at the level of individual neurons and their receptive fields, we would indeed need to treat this phase shift as a novel input. Nevertheless, for DyNR, conceived as an idealization of a biological system for encoding orientation information, we can safely assume that visual areas in biological organisms have a sufficient number of phase-sensitive simple cells and phase-indifferent complex cells to maintain the continuity of input to VWM.

      When comparing conditions with and without the phase shift of stimuli (Fig S1B), we found performance to be comparable in the perceptual condition (simultaneous presentation) and with the longest delay (1 second), suggesting that the phase shift did not change the visibility or encoding of information into VWM. In contrast, we found strong evidence that observers had access to an additional source of information over intermediate delays when the phase shift was not used. This was evident through enhanced recall performance from 0 ms to 400 ms delay. Based on this, we concluded that the additional source of information available in the absence of a phase shift was accessible immediately following stimulus offset and had a brief duration, aligning with the theoretical concept of retinal afterimages.

      (3) It seems odd that the mask does not interrupt sensory processing in Experiment 2. Isn't this the intended purpose of the mask? Should readers interpret this as all masks not being effective in disrupting sensory processing/iconic memory? Or is this specific to the mask used in the experiment?

      Visual masks are often described as instantly and completely halting the visual processing of information that preceded the mask. We also anticipated the mask would entirely terminate sensory processing, but our data indicate the effect was not complete (as indicated by model variants in Experiment 2). Nevertheless, we believe we achieved our intended goal with this experiment – we observed a clear modulation of response errors with changing stimulus duration, indicating that the post-stimulus information that survived masking did not compromise the manipulation of stimulus duration. Moreover, the DyNR model successfully accounted for the portion of signal that survived the mask.

      We can identify two possible reasons why masking was incomplete. First, it is possible that the continuous report measure used in our experiments is more sensitive than the discrete measures (e.g., forced-choice methods) commonly employed in experiments that found masks to be 100% effective. Second, despite using a flickering white noise mask at full contrast, it is possible that it may not have been the most effective mask; for instance, a mask consisting of many randomly oriented Gabor patches matched in spatial frequency to the stimuli could prove more effective. We decided against such a mask because we were concerned that it could potentially act as a new input to orientation-sensitive neurons, rather than just wiping out any residual sensory activity.

      (4) I apologize if I missed it, but the authors did not compare the DyNR model to a model without decaying sensory information for Experiment 1.

      We tested two DyNR variants in which the diffusion process was solely responsible for memory fidelity dynamics. These models assumed that the sensory signal terminates abruptly with stimuli offset, and the VWM signal encoding the stimuli was equal to the limit imposed by normalization, independent of the delay duration.

      As variants of this model failed to account for the observed response errors both quantitatively (see 'Fixed neural signal' under Model variants) and qualitatively (Figure S3), we decided not to test any more restrictive variants, such as the one without sensory decay and diffusion.

      (5) In the current model, selection is considered to be absolute (all or none). However, this need not be the case (previous work argues for graded selection). Could a model where memories are only partially selected, in a manner that is mediated by load, explain the load effects seen in behavior?

      Thank you for this point. If attentional selection was partial, it would affect the observers’ efficiency in discarding uncued objects to release allocated resources and encode additional information about the cued item. We and others have previously examined whether humans can efficiently update their VWM when previous items become obsolete. For example, Taylor et al. (2023) showed that observers could efficiently remove uncued items from VWM and reallocate the released resources to new visual information. These findings align with results from other studies (e.g., Ecker, Oberauer, & Lewandowsky, 2014; Kessler & Meiran, 2006; Williams et al., 2013).

      Based on these findings, we feel justified in assuming that observers in our current task were capable of fully removing all uncued objects, allowing them to continue the encoding process for the cued orientation that was already partially stored in VWM, such that the attainable limit on representational precision for the cued item equals the maximum precision of VWM.

      Partial removal could in principle be modelled in the DyNR model by introducing an additional plateau parameter specifying a maximum attainable precision after the cue. Our concern would be that such a plateau parameter would trade off with the parameter associated with Hick’s law (i.e., cue interpretation time). The former would control the amount of information that can be encoded into VWM, while the latter regulates the amount of sensory information available for encoding. We are wary of adding additional parameters, and hence flexibility, to the model where we do not have the data to sufficiently constrain them.

      Ecker, U. K. H., Oberauer, K., & Lewandowsky, S. (2014b). Working memory updating involves item-specific removal. Journal of Memory and Language, 74, 1–15. https://doi.org/10.1016/j.jml. 2014.03.006

      Kessler, Y., & Meiran, N. (2006). All updateable objects in working memory are updated whenever any of them are modified: Evidence from the memory updating paradigm. Journal of Experimental Psychology: Learning, Memory, and Cognition, 32, 570–585. https://doi.org/10.1037/0278-7393.32.3.570

      Taylor, R., Tomić, I., Aagten-Murphy, D., & Bays, P. M. (2023). Working memory is updated by reallocation of resources from obsolete to new items. Attention, Perception, & Psychophysics, 85(5), 1437–1451. https://doi.org/10.3758/s13414-022-02584-2

      Williams, M., & Woodman, G. F. (2012). Directed forgetting and directed remembering in visual working memory. Journal of Experimental Psychology. Learning, Memory, and Cognition, 38(5), 1206–1220. https://doi.org/10.1037/a0027389

      (6) Previous work, both from the authors and others, has shown that memories are biased as if they are acted on by attractive/repulsive forces. For example, the memory of an oriented bar is biased away from horizontal and vertical and biased towards diagonals. This is not accounted for in the current model. In particular, this could be one mechanism to generate a non-uniform drift rate over time. As noted in the paper, a non-uniform drift rate could capture many of the behavioral effects reported.

      The reviewer is correct that the model does not currently include stimulus-specific effects, although our work on that topic provides a clear template for incorporating them in future (e.g. Taylor & Bays, 2018). Specifically on the question of generating a non-uniform drift, we have another project that currently looks at this exact question (cited in our manuscript as Tomic, Girones, Lengyel, and Bays; in prep.). By examining various datasets with varying memory delays, including the Additional Dataset 1 reported in the Supplementary Information, we found that stimulus-specific effects on orientation recall remain constant with retention time. Specifically, although there is a clear increase in overall error over time, estimation biases remain constant in direction and amplitude, indicating that the bias does not manifest in drift rates (see also Rademaker et al., 2018; Figure S1).

      Taylor, R., & Bays, P. M. (2018). Efficient coding in visual working memory accounts for stimulus-specific variations in recall. The Journal of Neuroscience, 1018–18. https://doi.org/10.1523/JNEUROSCI.1018-18.2018

      Rademaker, R. L., Park, Y. E., Sack, A. T., & Tong, F. (2018). Evidence of gradual loss of precision for simple features and complex objects in visual working memory. Journal of Experimental Psychology: Human Perception and Performance. https://doi.org/10.1037/xhp0000491

      (7) Finally, the authors use AIC to compare many different model variants to the DyNR model. The delta-AICs are high (>10), indicating a strong preference for the DyNR model over the variants. However, the overall quality of fit to the data is not clear. What proportion of the variance in data was the model able to explain? In particular, I think it would be helpful for the reader if the authors reported the variance explained on withheld data (trials, conditions, or subjects).

      Thank you for this comment.

      Below we report the estimates of r2, representing the goodness of fit between observed data (i.e., RMSE) and the DyNR model predictions.

      In Experiment 1, the r2 values between observations and predictions were computed across delays for each set size, yielding the following estimates: r2ss1 = 0.60; r2ss4 = 0.87; r2ss10 = 0.95. Note that lower explained variance for set size 1 arises from both data and model predictions having near-constant precision.

      In Experiment 2, we calculated r2 between observations and predictions across presentation durations, separately for each set size, resulting in the following estimates: r2ss1 = 0.88; r2ss4 = 0.71; r2ss10 = 0.70. Note that in this case the decreasing percentage of explained variance with set size is a consequence of having less variability in both data and model predictions with larger set sizes.

      While these estimates suggest that the DyNR model effectively fits the psychophysical data, a more rigorous validation approach would involve cross-validation checks across all conditions with a withheld portion of trials. Regrettably, due to the large number of conditions in each experiment, we could only collect 50 trials per condition. We are sceptical that fitting the model to even fewer trials, as necessary for cross-validation, would provide a reliable assessment of model performance.

      Minor: It isn't clear to me why the behavioral tasks are shown in Figure 6. They are important for understanding the results and are discussed earlier in the manuscript (before Figure 3). This just required flipping back and forth to understand the task before I could interpret the results.

      Thank you for this comment. We have now moved the behavioural task figure to appear early in the manuscript (as Figure 3).

      Reviewer #3 (Recommendations For The Authors):

      (1) Dynamics of sensory signals during perception

      I believe that the modeled sensory signal is a reasonable simplification and different ways to model the decay function are discussed. I would like to ask the authors to discuss the implications of slightly more complex initial sensory transients such as the ones shown in Teeuwen (2021). Specifically for short exposure times, this might be particularly relevant for the model fits as some of the alternative models diverge from the data for short exposures. In addition, the role of feedforward (initial transient?) and feedback signaling (subsequent "plateau" activity) could be discussed. The first one might relate more strongly to sensory signals whereas the latter relates more to top-down attention/recurrent processing/VWM.

      Particularly, this latter response might also be sensitive to the number of items present on the screen which leads to a related question pertaining to the limitations of attention during perception. Some work suggests that perception is similarly limited in the amount of information that can be represented concurrently (Tsubomi, 2013). Could the authors discuss the implications of this hypothesis? What happens if maximum sensory amplitude is set as a free parameter in the model?

      Tsubomi, H., Fukuda, K., Watanabe, K., & Vogel, E. K. (2013). Neural limits to representing objects still within view. Journal of Neuroscience, 33(19), 8257-8263.

      Thank you for this question. Below, we unpack it and answer it point by point.

      While we agree our model of the sensory response is justified as an idealization of the biological reality, we also recognise that recent electrophysiological recordings have illuminated intricacies of neuronal responses within the striate cortex, a critical neural region associated with sensory memory (Teeuwen et al, 2021). Notably, these recordings reveal a more nuanced pattern where neurons exhibit an initial burst of activity succeeded by a lower plateau in firing rate, and stimulus offset elicits a second small burst in the response of some neurons, followed by a gradual decrease in activity after the stimulus disappears (Teeuwen et al, 2021).

      In general, asynchronous bursts of activity in individual neurons will tend to average out in the population making little difference to predictions of the DyNR model. Synchronized bursts at stimulus onset could affect predictions for the shortest presentations in Exp 2, however the model appears to capture the data very well without including them. We would be wary of incorporating these phenomena into the model without more clarity on their universality (e.g., how stimulus-dependent they are), their significance at the population level (as opposed to individual neurons), and most importantly, their prominence in visual areas outside striate cortex. Specifically, while Teeuwen et al. (2021) described activity in V1, our model does not make strong assumptions about which visual areas are the source of the sensory input to WM. Based on these uncertainties we believe the idealized sensory response is justified for use in our model.

      Next, thank you for the comment on feedforward and feedback signals. We have added the following to our manuscript:

      “Following onset of a stimulus, the visual signal ascends through visual areas via a cascade of feedforward connections. This feedforward sweep conveys sensory information that persists during stimulus presentation and briefly after it disappears (Lamme et al., 1998). Simultaneously, reciprocal feedback connections carry higher-order information back towards antecedent cortical areas (Lamme and Roelfsema, 2000). In our psychophysical task, feedback connections likely play a critical role in orienting attention towards the cued item, facilitating the extraction of persisting sensory signals, and potentially signalling continuous information on the available resources for VWM encoding. While our computational study does not address the nature of these feedforward and feedback signals, a challenge for future research is to describe the relative contributions of these signals in mediating transmission of information between sensory and working memory (Semedo et al., 2022).”

      Lamme, V. A., Supèr, H., & Spekreijse, H. (1998). Feedforward, horizontal, and feedback processing in the visual cortex. Current Opinion in Neurobiology, 8(4), 529–535. https://doi.org/10.1016/S0959-4388(98)80042-1

      Lamme, V. A. F., & Roelfsema, P. R. (2000). The distinct modes of vision offered by feedforward and recurrent processing. Trends in Neurosciences, 23(11), 571–579. https://doi.org/10.1016/S0166-2236(00)01657-X

      Semedo, J. D., Jasper, A. I., Zandvakili, A., Krishna, A., Aschner, A., Machens, C. K., Kohn, A., & Yu, B. M. (2022). Feedforward and feedback interactions between visual cortical areas use different population activity patterns. Nature Communications, 13(1), 1099. https://doi.org/10.1038/s41467-022-28552-w

      Finally, both you and Reviewer 2 raised a similar interesting question regarding capacity limitations of attention during perception Such a limitation could be modelled by freely estimating sensory amplitude and implementing divisive normalization to that signal, similar to how VWM is constrained. We can consider two potential mechanisms through which divisive normalization might be incorporated into sensory processing within the DyNR model.

      The first possibility involves assuming that normalization is pre-attentive. In this scenario, the sensory activity of each object would be rescaled at the lowest level of sensory processing, occurring before the allocation of attentional or VWM resources. One strong prediction of such an implementation is that recall error in the simultaneous cue condition (Experiment 1) should vary with set size. However, this prediction is inconsistent with the observed data, which failed to show a significant difference between set sizes, and is more closely aligned with the hypothesis of no-difference (F(2,18) = 1.26, p = .3, η2 = .04, BF10 = 0.47). On that basis, we anticipate that introducing normalization as a pre-attentive mechanism would impair the model fit.

      An alternative scenario is to consider normalization as post-attentive. In the simultaneous cueing condition, only one item is attended (i.e., the cued one), regardless of the displayed set size. Here, we would expect normalized activity for a single item, regardless of the number of presented objects, which would then be integrated into VWM. This expanded DyNR model with post-attentive normalization would make exactly the same predictions as the proposed DyNR for recall fidelity, so distinguishing between these models would not be possible based on working memory experiments.

      To acknowledge the possibility that sensory signals could undergo divisive normalization and to motivate future research, we have added the following to our manuscript:

      “As well as being implicated in higher cognitive processes including VWM (Buschman et al, 2011; Sprague et al., 2014), divisive normalization has been shown to be widespread in basic sensory processing (Bonin et al., 2005; Busse et al., 2009; Ni et al., 2017). The DyNR model presently incorporates the former but not the latter type of normalization. While the data observed in our experiments do not provide evidence for normalization of sensory signals (note comparable recall errors across set size in the simultaneous cue condition of Experiment 1), this may be because sensory suppressive effects are localized and our stimuli were relatively widely separated in the visual field: future research could explore the consequences of sensory normalization for recall from VWM using, e.g., centre-surround stimuli (Bloem et al., 2018).”

      Bloem, I. M., Watanabe, Y. L., Kibbe, M. M., & Ling, S. (2018). Visual Memories Bypass Normalization. Psychological Science, 29(5), 845–856. https://doi.org/10.1177/0956797617747091

      Bonin, V., Mante, V., & Carandini, M. (2005). The Suppressive Field of Neurons in Lateral Geniculate Nucleus. The Journal of Neuroscience, 25(47), 10844–10856. https://doi.org/10.1523/JNEUROSCI.3562-05.2005

      Buschman, T. J., Siegel, M., Roy, J. E., & Miller, E. K. (2011). Neural substrates of cognitive capacity limitations. Proceedings of the National Academy of Sciences, 108(27), 11252–11255. https://doi.org/10.1073/pnas.1104666108

      Busse, L., Wade, A. R., & Carandini, M. (2009). Representation of Concurrent Stimuli by Population Activity in Visual Cortex. Neuron, 64(6), 931–942. https://doi.org/10.1016/j.neuron.2009.11.004

      Ni, A. M., & Maunsell, J. H. R. (2017). Spatially tuned normalization explains attention modulation variance within neurons. Journal of Neurophysiology, 118(3), 1903–1913. https://doi.org/10.1152/jn.00218.2017

      Sprague, T. C., Ester, E. F., & Serences, J. T. (2014). Reconstructions of Information in Visual Spatial Working Memory Degrade with Memory Load. Current Biology, 24(18), 2174–2180. https://doi.org/10.1016/j.cub.2014.07.066

      (2) Effectivity of retro-cues at long delays

      Can the authors discuss how cues presented at long delays (>1000 ms) can still lead to increased memory fidelity when sensory signals are likely to have decayed? A list of experimental work demonstrating this can be found in Souza & Oberauer (2016).

      Souza, A. S., & Oberauer, K. (2016). In search of the focus of attention in working memory: 13 years of the retro-cue effect. Attention, Perception, & Psychophysics, 78, 1839-1860.

      The increased memory fidelity observed with longer delays between memory array offset and cue does not result from integrating available sensory signals into VWM because the sensory signal would have completely decayed by that time. Instead, research so far has indicated several alternative mechanisms that could lead to higher recall precision for cued items, and we can briefly summarize some of them, which are also reviewed in more detail in Souza and Oberauer (2016).

      One possibility is that, after a highly predictive retro-cue indicates the to-be-tested item, uncued items can simply be removed from VWM. This could result in decreased interference for the cued item, and consequently higher recall precision. Secondly, the retro-cue could also indicate which item can be selectively attended to, and thereby differentially strengthening it in memory. Furthermore, the retro-cue could allow evidence to accumulate for the target item ahead of decision-making, and this could increase the probability that the correct information will be selected for response. Finally, the retro-cued stimulus could be insulated from interference by subsequent visual input, while the uncued stimuli may remain prone to such interference.

      A neural account of this retro-cue effect based on the original neural resource model has been proposed in Bays & Taylor, Cog Psych, 2018. However, as we did not use a retro-cue design in the present experiments, we have decided not to elaborate on this in the manuscript.

      (3) Swap errors

      I am somewhat surprised by the empirically observed and predicted pattern of swap errors displayed in Figure S2. For set size 10, swap probability does not consistently increase with the duration of the retention interval, although this was predicted by the author's model. At long intervals, swap probability is significantly higher for large compared to small set sizes, which also seems to contrast with the idea of shared, limited VWM resources. Can the authors provide some insight into why the model fails to reproduce part of the behavioral pattern for swap errors? The sentence in line 602 might also need some reconsideration in this regard.

      Determining the ground truth for swap errors poses a challenge. The prevailing approach has been to employ a simpler model that estimates swap errors, such as a three-component mixture model, and use those estimates as a proxy for ground truth. However, this method is not without its shortcomings. For example, the variability of swap frequency estimates tends to increase with variability in the report feature dimension (here, orientation). This is due to the increasing overlap of response probability distributions for swap and non-swap responses. Consequently, the discrepancy between any two methods of swap estimation is most noticeable when there is substantial variability in orientation reports (e.g., 10 items and long delay or short exposure).

      When modelling swap frequency in the DyNR model, our aim was to provide a parsimonious account of swap errors while implementing similar dynamics in the spatial (cue) feature as in the orientation (report) feature. This parametric description captured the overall pattern of swap frequency with set size and retention and encoding time, but is still only an approximation of the predictions if we fully modelled memory for the conjunction of cue and report features (as in e.g. Schneegans & Bays, 2017; McMaster et al, 2020).

      We expanded the existing text in the section ‘Representational dynamics of cue-dimension features’ of our manuscript:

      “… Although we did not explicitly model the neural signals representing location, the modelled dynamics in the probability of swap errors were consistent with those of the primary memory feature. We provided a more detailed neural account of swap errors in our earlier works that is theoretically compatible with the DyNR model (McMaster et al., 2020; Schneegans & Bays, 2017).

      The DyNR model successfully captured the observed pattern of swap frequencies (intrusion errors). The only notable discrepancy between DyNR and the three-component mixture model (Fig. S2) arises with the largest set size and longest delay, although with considerable interindividual variability. As the variability in report-dimension increases, the estimates of swap frequency become more variable due to the growing overlap between the probability distributions of swap and non-swap responses. This may explain apparent deviations from the modelled swap frequencies with the highest set size and longest delay where orientation response variability was greatest. “

      McMaster, J. M. V., Tomić, I., Schneegans, S., & Bays, P. M. (2022). Swap errors in visual working memory are fully explained by cue-feature variability. Cognitive Psychology, 137, 101493. https://doi.org/10.1016/j.cogpsych.2022.101493

      Schneegans, S., & Bays, P. M. (2017). Neural Architecture for Feature Binding in Visual Working Memory. The Journal of Neuroscience, 37(14), 3913–3925. https://doi.org/10.1523/JNEUROSCI.3493-16.2017

      (4) Direct sensory readout

      The model assumes that readout from sensory memory and from VWM happens with identical efficiency. Currently, we don't know if these two systems are highly overlapping or are fundamentally different in terms of architecture and computation. In the case of the latter, it might be less reasonable to assume that information readout would happen at similar efficiencies, as it is currently assumed in the manuscript. Perhaps the authors could briefly discuss this possibility.

      In the direct sensory read-out model, we did not explicitly model the efficiency of readout from either sensory or VWM store. However, the distinctive prediction of this model is that the precision of recall changes exponentially with delay at every set size, including one item. This prediction does not depend on the relative efficiency of readout from sensory and working memory, but only on the principle that direct readout from sensory memory bypasses the capacity limit on working memory. This prediction is inconsistent with the pattern of results observed in Experiment 1, where early cues did not show a beneficial effect on recall error for set size 1. While the proposal raised by the reviewer is intriguing, even if we were to model the process of readout from both the sensory and VWM stores with different efficiencies, the direct read-out model could not account for the near-constant recall error with delay for set size one.

      (5) Encoding of distractors

      One of the model assumptions is that, for simultaneous presentations of memory array and cue only the cued feature will be encoded. Previous work has suggested that participants often accidentally encode distractors even when they are cued before memory array onset (Vogel 2005). Given these findings, how reasonable is this assumption in the authors' model?

      Vogel, E. K., McCollough, A. W., & Machizawa, M. G. (2005). Neural measures reveal individual differences in controlling access to working memory. Nature, 438(7067), 500-503.

      Although previous research suggested that observers can misinterpret the pre-cue and encode one of the uncued items, our results argue against this being the case in the current experiment. Such encoding failures would manifest in overall recall error, resulting in a gradient of error with set size, owing to the presence of more adjacent distractors in larger set sizes. However, when we compared recall errors between set sizes in the simultaneous cue condition, we did not find a significant difference between set sizes, and moreover, our results were more likely under the hypothesis of no-difference (F(2,18) = 1.26, p = .3, η2 = .04, BF10 = 0.47). If observers occasionally encoded and reported one of the uncued items in the simultaneous cue condition, those errors were extremely infrequent and did not affect the overall error distributions.

  3. learn-us-east-1-prod-fleet01-xythos.content.blackboardcdn.com learn-us-east-1-prod-fleet01-xythos.content.blackboardcdn.com
    1. o be a person is to be a voice that cannotproperly be ignored, a voice which speaks to issues raised in commonwith others and which speaks with a certain authority: enough author-ity, certainly, for discord with that voice to give others reason to pauseand thin

      That is the benefit of democracy that each person has a voice that matters and that can choose where they go as a country.

  4. 3ad5c237-7dcf-4014-b052-345b96b6dcf6.filesusr.com 3ad5c237-7dcf-4014-b052-345b96b6dcf6.filesusr.com
    1. Análisis dimensional

      El análisis dimensional es muy importante, este nos ayuda como bien dice en el texto, cuando no recordamos bien una formula y para verificar que lo que estamos haciendo sea congruente, ya que si estoy usando una formula donde despeje para que me quedara volumen, las unidades deben ser metros cúbicos, centímetros cúbicos o litros, no me pueden quedar unidades de tiempo o de velocidad, porque no seria congruente.

    1. Figure O.5 shows an interesting balance of how refugees affect an economy and how their lives are likely to turn out based on motive. I think the most interesting part about it is how motive can strongly affect success. If they are moving to a country that has job opportunities for them, and they are moving for those opportunities, they are likely to be more successful than if they are running away. https://www.weforum.org/agenda/2024/01/migration-model-sustainable-development/ this article by the World Economic Forum explains why this model is true, and how it helps development of a country in the long run.

    1. TÚI VẢI CHĂN GA CÓ LỢI ÍCH - GIẢI PHÁP LƯU TRỮ TIỆN LỢI

      Chăn ga gối nệm là những vật dụng cần thiết trong mỗi gia đình. Tuy nhiên, việc cất giữ chăn ga gối nệm không đúng cách sẽ khiến chúng bị bám bụi, ẩm mốc, thậm chí là hư hỏng. Túi vải đựng chăn ga là một giải pháp lưu trữ tiện lợi, giúp bảo vệ chăn ga gối nệm khỏi bụi bẩn, ẩm mốc và là giải pháp MKT hiệu quả cho các doanh nghiệp vậy túi vải chăn ga có lợi ích

      Túi vải đựng chăn ga là gì? 

      Túi vải đựng chăn ga là một loại túi được làm từ chất liệu vải, có tác dụng đựng chăn ga gối nệm. Túi vải thường có kích thước lớn, giúp đựng được nhiều chăn ga gối nệm cùng lúc. Ngoài ra, túi vải còn có khả năng chống thấm nước, chống bụi bẩn và ngăn ngừa ẩm mốc, giúp bảo vệ chăn ga gối nệm khỏi những tác nhân gây hại từ môi trường và lợi ích túi vải đựng chăn ga

      Túi vải đựng chăn ga được sử dụng phổ biến trong các gia đình, giúp lưu trữ chăn ga gối nệm gọn gàng, ngăn nắp và sạch sẽ. Ngoài ra, túi vải đựng chăn ga in logo còn là giải pháp MKT giúp các doanh nghiệp định vị được thương hiệu, nâng tầm giá trị thương hiệu

      Túi vải đựng chăn ga làm từ nguyên vật liệu gì? 

      Túi vải đựng chăn ga được làm từ nhiều loại vật liệu khác nhau, tùy thuộc vào nhu cầu và sở thích của người sử dụng. Dưới đây là một số loại vật liệu phổ biến được sử dụng để làm túi vải:

      Vải không dệt: Vải không dệt là loại vải được làm từ các sợi tổng hợp, có khả năng chống thấm nước, chống bụi bẩn và ngăn ngừa ẩm mốc. Vải không dệt có giá thành rẻ, nhẹ, dễ dàng gấp gọn. Tuy nhiên, vải không dệt có độ bền kém hơn so với các loại vải khác.

      Vải bố: Vải bố là loại vải được làm từ sợi gai, có độ bền cao, chống thấm nước tốt. Vải bố có trọng lượng nặng hơn so với các loại vải khác.

      Vì sao nên sử dụng túi vải đựng chăn ga? 

      Có rất nhiều lý do để bạn nên sử dụng túi vải đựng chăn ga. Dưới đây là một số lý do phổ biến nhất:

      Bảo vệ chăn ga khỏi bụi bẩn, ẩm mốc: Túi vải được làm từ chất liệu vải dày dặn, có khả năng chống thấm nước, chống bụi bẩn và ngăn ngừa ẩm mốc. Nhờ đó, chăn ga của bạn sẽ được bảo vệ tốt khỏi những tác nhân gây hại từ môi trường.

      Tiết kiệm diện tích: Túi vải có kích thước lớn, giúp bạn đựng được nhiều chăn ga gối nệm cùng lúc. Ngoài ra, bạn có thể gấp gọn túi vải khi không sử dụng, giúp tiết kiệm diện tích cho căn phòng.

      Tiện lợi, dễ sử dụng: Túi vải có thiết kế đơn giản, dễ dàng mở ra đóng vào. Bạn chỉ cần mở miệng túi ra, cho chăn ga gối nệm vào và kéo khóa lại là xong.

      Các loại túi vải đựng chăn ga

      Trên thị trường hiện nay có nhiều loại túi vải đựng chăn ga với đa dạng mẫu mã, kích thước và chất liệu. Dưới đây là một số loại túi vải phổ biến:

      Túi vải bằng vải không dệt: có ưu điểm là giá thành rẻ, nhẹ, dễ dàng gấp gọn. Tuy nhiên, túi vải không dệt có độ bền kém hơn so với các loại túi vải khác.

      Túi vải bằng vải dù: có ưu điểm là độ bền cao, chống thấm nước tốt và có nhiều màu sắc, họa tiết trang trí.

      Lựa chọn túi vải đựng chăn ga phù hợp

      Khi lựa chọn túi vải đựng chăn ga, bạn cần lưu ý một số yếu tố sau:

      Kích thước túi: Bạn cần lựa chọn túi vải có kích thước phù hợp với số lượng chăn ga gối nệm cần đựng.

      Chất liệu túi: Bạn nên lựa chọn túi vải làm từ chất liệu bền, có khả năng chống thấm nước, chống bụi bẩn và ngăn ngừa ẩm mốc.

      Mẫu mã túi: Bạn có thể lựa chọn túi vải có mẫu mã, màu sắc phù hợp với sở thích và không gian nội thất của gia đình.

      Làm túi vải đựng chăn ga in logo ở đâu? 

      Nếu bạn đang tìm kiếm một địa chỉ uy tín để in  túi vải đựng chăn ga, thì Túi Vải Việt Paper Life là một lựa chọn hoàn hảo dành cho bạn. Túi Vải Việt Paper Life là một trong những nhà sản xuất và cung cấp túi vải hàng đầu tại Việt Nam. Với kinh nghiệm lâu năm trong ngành, Túi Vải Việt Paper Life đã cho ra đời nhiều sản phẩm túi vải đựng chăn ga với chất lượng cao, mẫu mã đa dạng và giá thành cạnh tranh.

      Dưới đây là một số lợi ích khi in túi vải đựng chăn ga tại Túi Vải Việt Paper Life:

      Chất lượng cao: Túi vải tại Túi Vải Việt Paper Life được làm từ chất liệu vải cao cấp, có độ bền cao, chống thấm nước, chống bụi bẩn và ngăn ngừa ẩm mốc. Nhờ đó, chăn ga gối nệm của bạn sẽ được bảo vệ tốt khỏi những tác nhân gây hại từ môi trường.

      Mẫu mã đa dạng: Túi vải tại Túi Vải Việt Paper Life có nhiều mẫu mã khác nhau, từ đơn giản đến sang trọng, phù hợp với mọi sở thích và nhu cầu của khách hàng.

      Giá thành cạnh tranh: Túi vải tại Túi Vải Việt Paper Life có giá thành cạnh tranh, phù hợp với túi tiền của nhiều người tiêu dùng.

      Ngoài ra, khi mua túi vải tại Túi Vải Việt Paper Life bạn còn nhận được nhiều ưu đãi hấp dẫn.

    1. O problema de gerar todos os conceitos formais e classificá-los hierarquicamente apre-senta um comportamento exponencial no pior caso[22]. Apesar desse comportamento serraramente encontrado em casos práticos [18], ainda assim o custo computacional pode serproibitivo. Esse alto custo computacional justifica o estudo de algoritmos e abordagens al-ternativas para geração dos conceitos formais e construção do reticulado conceitual

      Problema

    1. Chào mọi người, em xin chia sẻ về một người Thầy dạy em nhiều điều trong chứng khoán1) Thầy ấy rất hay khoe lãi lên facebook, lại còn là một Giám đốc học thuật của một trung tâm nên em rất tin tưởng. Địa điểm học tập là ở Tòa Nhà Ban Tuyên Giáo Q3 Nguyễn Đình Chiểu. Đặc điểm của Thầy là profile rất nice, hay nói về đạo lý và nước hoa và khoe body của Thầy (dù nó béo và đầy lipit)2) Năm 2022, Thầy ấy kêu gọi mọi người mua NLG all in đến dưới 69 full margin TP80, sau đó nó sập về 30, à, thế là cháy mất rồi. Sau đó Thầy bảo là chỉ chịu trách nhiệm hết t+3 thôi. Sau đó Thầy bảo là do xui, ra tin bắt anh Quyết thì phải chạy chứ. Thầy call ITA full margin sau đó Chị Yến bắt.3) Sau đó Thầy call PDR từ 15 nó sập về 10 sau khi nó hồi lên 14, Thầy bảo có thể còn biến số nên giảm vị thế đi, thế là nó lên 30. Thầy gáy nhân 3 nhưng hàng không biết Thầy còn cầm không4) 9 tháng trước, Thầy phân tích rất kỹ càng rồi call học viên mua AGG giá 28, giá sau đó lên 36 thì bị đạp, nhưng đạp thì Thầy vẫn bảo mọi người giữ, giữ đến 24 Thầy hỏi còn margin cho Thầy mua không và giờ nó đang có giá 21-22. Thầy phân tích AGG rất kỹ, kỹ tới nỗi Market tăng 250 điểm, BDS tăng 20 30% thì AGG từ 36 về 20. 5) Chuyện sẽ chẳng là gì nếu- Thầy bảo do xui nhưng bản chất Thầy call học viên mua cho quỹ xả, lần 2 Thầy call cho Thầy xả- Thầy bảo Quỹ Nhật vào mua AGG, Thầy nói The Sóng book lợi nhuận nhưng thì ra Thầy book lợi nhuận trên đầu con dân- Chuyện xảy ra Thầy bảo là do bạn học viên call chứ Thầy không call. Bằng bùa lợi Satire/Parody mang trên người Thầy có quyền nói mọi thứ chỉ là chế giễu thôi.- Năm 2023, Thầy call short Bank, Bank tăng, Thầy chê BTC nhưng không dám bet kèo 30 BTC cho ETF được duyệt khi có người thách.- Thầy bảo lớp được xem full danh mục, báo trước, khi có cức mà Thầy cho xem, mà chắc gì là tài khoản của Thầy hay Thầy bảo skin in the game nhưng ai biết là bỏ 500 đồng hay 500 đô. Mình viết bài này ra đây là để mọi người cẩn thận với Thầy, à mà nghe đồn Thầy từng bị trường R đuổi vì không đạt KPI, Thầy làm trái phiếu thì sai pháp lý phải làm lại, Thầy lấy profile 1 trường bên NZ nhưng chỉ là profile liên kết, chứ Thầy làm gì có bằng PhD để trường M bên NZ tuyển chính thức. À trung thâm của Thầy lùa đủ thứ, lùa quản lý tài sản, lùa CFA dù chả khác gì sách nói, lùa MA dù Thầy toàn chém gió lại.Mọi người copy share thoải mái, để người ta không còn bị lùa và để cho người ta thấy uy tín của Thầy như cái chart AGG vậy đó: Cấm thủng lòng đất

      Tai Tran?

    1. ¿Cuántas personas conforman tu lugar de trabajo?

      ¿Ésta pregunta podría ser un número? porque creo que aquí podemos tener empresas o negocios pequeños. Si no se puede, entonces sugiero incluir un rango de menos de 5 personas.

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

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      In this manuscript Burban et al explore the effect of the mitochondrial oxidative phosphorylation (OXPHOS) inhibitor Mubritinib on patient derived glioblastoma stem cells and murine xenografts. The authors first show that i) Mubritinib is an inhibitor of OXPHOS in brain tumor stem cells (BTSC), ii) that it impairs cell growth and self-renewal of patient-derived BTSC with different genetic background and iii) has an effect on the expression of genes related to stemness. In addition, the authors convincingly show that Mubritinib is a brain penetrant drug, and by transplanting luciferase expressing BTSC into the brain of immunodeficient mice they show it delays GB tumorigenesis and the animal lifespan (either alone, or more efficiently if combined with IR treatment). Finally, by performing toxicological and behavioral studies in mice models, Burban et al demonstrate that Mubritinib has a well-tolerated and safe profile and does not induce damage to healthy cells.

      The manuscript is well written and organized and the data is clearly presented. The results are convincing, but a few additional experiments and controls would be beneficial to support the claims of the paper, most of which are easily addressable.

      Main comments:

      • Finding suitable control cells for BTSC experiments is a widely acknowledged challenge in the field. However, in line with other studies, it is recommended that the authors consider using a non-oncogenic NSC as control line to demonstrate that the effects reported in Figure 1 and Figure 2 are more pronounced in BTSC compared to NSC (as it was done in Suppl Fig3).
      • Figure 5 presents a significant finding indicating that Mubritinib enhances the sensitivity of GB tumors to IR. Considering that Temozolomide (TMZ) is the primary chemotherapy drug for GB patients, it would be crucial to investigate the potential outcomes of a combined treatment involving Mubritinib and TMZ. This will help determine if the combination exhibits promising results, comparable to what is demonstrated in Figures 5d, 5g, and 5i for Mubritinib and IR. Such experiment would reinforce the drug's potential for clinical trials in GB treatment.

      Minor comments:

      • The authors should specify early in the paper what is the number of samples of patient-derived BTSC they use and the fact that their genetic mutations are known (this information is summarized in the supplemental table 1, but only reported later in the manuscript). This information is important and should be clearly stated at the beginning of the manuscript.
      • In Figure 2a the inhibition at 20nM is significant but not very pronounced. Based on Figure 1 I would have expected to see a stronger effect at this concentration range. Can the authors comment/provide an explanation for this discrepancy?
      • The EdU incorporation experiment presented in Figure2h-I should be repeat with lower concentrations of the drug (in most of the assays the effect of Mubritinib is detectable at much lower concentrations).
      • Since the authors have done RNA-seq on the samples why don't they report the specific subtypes of their samples in the text and in Suppl Table 1 (Proneural, Neural, Classical or Mesenchymal) ? It is known that different molecular subtypes respond differently to treatments; therefore this information would be essential to understand if Mubritinib is effective on a wide range of GB subtypes.
      • In Figure2b and Supplemental Figure1b-c : instead of correlating the effect with genetic mutations, it would be more relevant if the authors could correlate the data with the molecular subtypes inferred by RNA-seq (see my comment above)
      • Regarding the RNA-seq experiment the authors should report what is the percentage (and numbers) of genes that change expression. Is there for example a preference for up- or down- regulation? It would be interesting to see a Gene Ontology (GO) analysis for the up-regulated genes versus a GO analysis of the down-regulated genes to confirm that the relevant categories show dysregulation as expected (e.g. enrichment for cell cycle and stemness genes in the down-regulated list, etc ).
      • In Figure2 m-o the difference between CTL and Mubritinib treated cells do not seem substantial, although it is shown as statistically relevant. Can the authors specify the percentage to be able to better assess the differences?
      • Add p-value for Figure3a-c
      • In the western blot in Supplemental Figure 3b Vinculin shows twice
      • Change" Given that Mubritinib is already completed a phase I clinical trial" into "...has completed..."

      Referees cross-commenting

      I agree with other reviewers that more data is needed to determine if mubritinib could be an effective treatment for various GB subtypes. The models used in this study do not encompass the full spectrum of GBM genetics. The authors should repreat the experiments using models that represent the major genetic/transcriptional subtypes of GBMs and clearly label and identify them in the study. Specifically, the authors should include models like 'classical/EGFR-amplified', 'mesenchymal', 'proneural/PDGFR amplified'. Alternatively, it is advisable to refrain from asserting that mubritinib is effective across genetic alterations in the manuscript.

      Significance

      Considering the limited effectiveness of existing treatments, it is crucial to explore alternative approaches to improve patient outcomes. This study demonstrates promising potential for the clinical translation of Mubritinib in GB treatment.

      A major limitation of this study is the narrow numbers of patient-derived samples used and absence of a proper control cell line. Unfortunately, as evidenced by the existing literature in the field, selecting a control cell line for glioma stem cells research is challenging due to the unknown cell-of-origin for this type of tumor. In addition, all the toxicity/safety tests were performed in mice models and it is difficult to predict how this would translate into human patients. However, the fact that a phase I clinical trial has already been completed for Mubritinib (in the context of a different type of tumor) is encouraging.

    1. prendizaje que se evidencia como proceso en las situacionesde cambio de algún elemento sustancial.

      Evidencia de aprendizaje en tres vertientes: a) aumento de capacidades profesionales y personales b) productos como métodos de trabajo, saberes técnicos o tecnologías innovadoras c) aumento de expectativas de supervivencia y desarrollo de la organización

    1. 12% of allogeneic, and 1% of autologous, HSCT (haematopoietic stem cell transplantation) recipients

      Some recent studies have found lower incidences (e.g. 8%) in allogeneic HSCT recipients.

      Invasive Aspergillosis in Allogeneic Hematopoietic Stem Cell Transplantation Recipients: A Large Cohort Single-Center Study. Yuliya A. Rogacheva, Vladislav V. Markelov, Marina O. Popova, et al. Blood. 2021; 138 (Suppl 1): doi.org/10.1182/blood-2021-153762.

    1. Tu mettrais l’univers entier dans ta ruelle,Femme impure ! L’ennui rend ton âme cruelle.Pour exercer tes dents à ce jeu singulier,Il te faut chaque jour un cœur au râtelier.Tes yeux, illuminés ainsi que des boutiquesOu des ifs flamboyants dans les fêtes publiques,Usent insolemment d’un pouvoir emprunté,Sans connaître jamais la loi de leur beauté.Machine aveugle et sourde, en cruautés féconde !Salutaire instrument, buveur du sang du monde,Comment n’as-tu pas honte et comment n’as-tu pasDevant tous les miroirs vu pâlir tes appas ?La grandeur de ce mal où tu te crois savanteNe t’a donc jamais fait reculer d’épouvante,Quand la nature, grande en ses desseins cachés,De toi se sert, ô femme, ô reine des péchés,— De toi, vil animal, — pour pétrir un génie ?Ô fangeuse grandeur ! sublime ignominie !
    1. 5-Stage Model; communities of inquiry; Social Presence; Teaching Presence; Cognitive Presence

      O modelo em 5 critérios que está inscrito em Keywords parece-me ser a chave para a permanente reflexão sobre processo de ensino-aprendizagem e de investigação, em qualquer um dos ambientes onde ocorra. Nesse sentido as e-actividades a serem delineadas, deverão decorrer de pressupostos comunicativos, participativos e colaborativos das acções, tendo em conte os diversos papeis a desempenhar pelos vários participantes em cada etapa e/ou fase. Parece-me não se poder prescindir do professor, supervisor no desenvolvimento do seu papel como motivador, moderador, co-participitante no processo.

    1. o simulatesuch a few-shot learning setting, we have devel-oped a new benchmark dataset, called FEWSHOT-WOZ, based on the MultiWOZ (Budzianowskiet al., 2018) and Cambridge NLG datasets (Wenet al., 2016a). F

      Để mô phỏng được cài đặt học máy few-shot, một bộ dữ liệu mẫu mới, gọi là FEWSHOT-WOZ đã được xây dựng.

    1. o,

      En la siguiente expresión después de ":" escribe "\ " … es un slash y un espacio, eso permitirá que el punto y coma no esté tan pegado a T. Realiza esto por favor en cada expresión igual a esta. En la Definición 4.3 los espacios son adecuados en la expresión {X(t) : t \in T}.

    1. Character space

      Al conjunto de todos los caracteres, es decir Character, le estamos enviando el mensajes space, lo cual nos entrega un conjunto dentro de ese conjunto. En este caso, estamos enviando el mensaje a un conjunto, lo cual se reconoce porque su primera letra es mayúscula. Si fuera minúscula, se la estaria enviando a un elemento de un conjunto. A los conjuntos se les conoce como clases, a los elementos se les conoce como instancias.

      A veces puede pasar que le enviemos un mensaje a una clase o una instancia y que el resultado caiga en otra instancia.

      1 to: 10

    1. For this is the chief and special point in their praises of Manichæus, that the divine mysteries which were taught figuratively in books from ancient times were kept for Manichæus, who was to come last, to solve and demonstrate; and so after him no other teacher will come from God, for he has said nothing in figures or parables, but has explained ancient sayings of that kind, and has himself taught in plain, simple terms. Therefore, when the Manichæans hear these words of their founder, on one side and border of the shining and sacred region was the region of darkness, they have no interpretations to fall back on

      Mani prided himself on speaking w/o parables, w/o figure, but in plain terms. He is the interpreter. Yet, Augustine points out that this leaves him with no where to go whenever his words fall short of the truth.

      So is it that Jesus / Catholics speak in figures so as to be able to slip out of intellectual stalemates? No - see Joseph Ratzinger's treatment on form vs content.

    2. we cannot know it as a fact of experience or as a truth of the understanding

      Augustine posits two sources of knowledge which one can arrive at w/o authority: experience and deduction from what we already know.

    1. Author Response

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

      Reviewer #1

      More details about the classification and how it is trained

      We included a sentence in the introduction to clarify which data we are using: "In order to demonstrate this improvement, we apply our methods to two classification datasets: a synthetic dataset and a public clinical dataset where the predicted outcome is the survival of the patient"

      And about how the classifier is trained in the "Results" section: "we used the default parameters of the classifier, since our focus is comparing the different imputation methods"

      Availability of the code

      Now the code is publicly available in a github repository https://github.com/AstraZeneca/dpp_imp/ (see Availability of Data and Code section)

      Reviewer #2

      Clarifying that Determinantal Point Processes and their deterministic version have been introduced before but are applied for the first time for data imputation in this work:

      We added explanation in the 6th paragraph of the introduction that we use pre-existing DPP and deterministic-DPP algorithms for our imputation methods and include the references to avoid confusion

      We also added a paragraph at the end of the introduction to summarize this work's contribution

      Explaining the claim about the computational advantage of using quantum determinantal point processes for the imputation methods:

      In the fourth paragraph of the "Discussion" section (page 8), we give an imputation example by numerically comparing the classical and quantum algorithms running time for DPP sampling, which shows the advantage of using the quantum algorithm.

      Regarding running time for classical DPP and quantum DPP sampling algorithms:

      We included Table VIII (page 13) that compares the preprocessing and sampling complexities for both classical and quantum DPP algorithms, we consider the case where we sample d rows from an (n,d) matrix and n=O(d) which is usually the case for our DPP-Random Forest algorithm

      We added some details regarding the quantum advantage in the first paragraph of page 12

      Regarding the comment about the modest improvement of the DPP methods and questions about their practical benefit:

      As mentioned in the third paragraph of the "Discussion" section, we point out that the consistency of the improvement and the removal of variance as a result of using the DPP and deterministic DPP methods make our methods very beneficial to use on clinical data. Further exploration with different data sets can provide a more result in a more complete understanding of the practical advantages of the methods

      Algorithmic complexity of the deterministic DPP algorithm:

      Detailed in the last sentence of the "Determinantal Point Processes" subsection of the "Methods" section: O(N^2 d) for the preprocessing step and O(Nd^3) for the sampling step

      Running time for the quantum deterministic DPP sampling and how it is done in practice:

      While it is difficult to assess the real running time for the quantum detDPP algorithm for large circuits (100 or more qubits), due to the unavailability of such devices, we give more details about our practical implementation in the last paragraph of the "Methods" section. In our case (up to 10 qubits) we used 1000 shots to sample the highest probability elements.

      On which quantum simulator was used

      We point out in the first paragraph of page 5 that we employ the qiskit noiseless simulator

    1. In the case of books — and, mutandis mutandis, other information resources — , there is no lack of characteristics that can serve as the basis for the definition of classes. To cite but a few examples, classifications of books can, in principle, be constructed around their physical size; the nature of their binding; their date of publication; their place of publication; the names of their authors or, should these be lacking, their titles; the subjects whereof they treat; the genres of writing that they represent; the languages in which they are written; the audiences for which they are written; or their provenance (cf. Bliss 1939, 23; Cutter 1904, 15; Hulme 1950 [1911–1912], 4–5, with Dousa 2017; Richardson 1901, 60–65). Historically, however, library classifications have tended to be based on a limited set of bibliographic attributes — namely, the → subject content and/or literary form of books (Bliss 1939, 24; Cutter 1904, 16; Hulme 1950 [1911–1912], 5; Mills 1968, 3). For this reason, they are sometimes referred to as “subject-classification[s]” (Bliss 1939, 25) or “subject classification schemes” (e.g., IFLA Working Group on Guidelines for National Bibliographic Agencies 2012, 22; Hider 2012, 162–170). Insofar as the subjects of books constitute objects of knowledge, some commentators have also characterized them as “knowledge organization classification systems” (Beghtol 2010). Yet if subject content and literary form have tended to be the primary foundations upon which library classifications have been built, one should not overlook the fact that, very often, some other attributes, such as the names of authors and date of publication, have served as principles for the sub-arrangement of books and other items within classes (cf. Sayers 1955, 14) and that physical features, such as size, have often governed the actual arrangement of books on shelves (cf. Brown 1898, 102–103; Mills 1968, 2). Very few, if any, library classifications have been, in practice, pure subject classifications.

      Materialidade do livro impõe vários indexicais, o que não se passa com o documento e a informação

    1. El nivel de desarrollo de los estudiantes en lenguaje puede ser a causa de la poca cantidad de bibliotecas en establecimientos educativos, solo el 5,7% cuenta con una biblioteca escolar, un porcentaje muy bajo para alcanzar los niveles mínimos de conocimientos. El texto menciona que popularmente se considera a las matemàticas como más complejas, esto se puede atribuir a que no existe un incentivo adecuado, o en su defecto un estudio de campo que ayude a determinar que procesos puedan ayudar a que los estudiantes se interesen genuinamente por la lectura.

    2. Es por esta razón, que los padres de familia, se ven obligados a buscar un pre universitario para los estudiantes de 3 de bachillerato porque se ven en la desesperación de que sus hijos en el colegio no aprenden las bases necesarias, y eso se debe a falencias que existen en los planes de trabajo, de los ministerios o instituciones, que no enseñan lo primordial, o lo más importante o muchas más no se actualizan, para enseñar lo de la actualidad.

    3. Estos resultados son una alerta para empezar a tomar conciencia de que en el Ecuador no se están trabajando las macrodestrezas lingüísticas. Además, la inexistencia de bibliotecas escolares en una gran cantidad de instituciones educativas resulta preocupante. ¿A dónde pueden acudir los estudiantes cuando quieren leer? Por otro lado, hay casos en los que hay bibliotecas, pero sin bibliotecarios que direccionen o den sugerencias de lecturas. Adicionalmente, esta noticia hace un llamado de atención al Ministerio de Educación para que invierta en espacios de lectura a los cuales la comunidad educativa pueda acceder.

    4. Sin el ánimo de justificar los datos expresados en el periódico, es preciso recordar que también se está evaluando en estos resultados el trabajo desarrollado en pandemia, donde tuvimos que bajar el nivel de complejidad, y quienes no podían ingresar a clases por falta de dispositivos electrónicos o internet, no practicaron adecuadamente el desarrollo de las habilidades expresivas. Recuerdo que en el año lectivo 2020-2021 debíamos recibir los trabajos que realizaban los estudiantes, pocos o muchos y la calificación no podía bajar de 7. Hoy vemos esas consecuencias. También, creo que la reducción del presupuesto del estado en educación influye en estos resultados. El gobierno ha presentado proyectos a los que no les dado un verdadero seguimiento.

    1. Motivational Force = E P × Ʃ[(P O) × V ]

      Motivational force --> dependent upon the expectancy, instrumentality and valence of a particular task or job

    Annotators

    1. Author Response

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

      eLife assessment:

      The authors report a novel hepatic lncRNA FincoR regulating FXR with therapeutic implications in the treatment of MASH. The findings are important and use an appropriate methodology in line with the current state-of-the-art, with convincing support for the claims.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In the article titled "Hammerhead-type FXR agonists induce an eRNA FincoR that ameliorates nonalcoholic steatohepatitis in mice," the authors explore the role of the Farnesoid X Receptor (FXR) in treating metabolic disorders like NASH. They identify a new liver-specific long non-coding RNA (lncRNA), FincoR, regulated by FXR, notably induced by agonists such as tropifexor. The study shows that FincoR plays a significant role in enhancing the efficacy of tropifexor in mitigating liver fibrosis and inflammation associated with NASH, suggesting its potential as a novel therapeutic target. The study makes a promising contribution to understanding the role of FincoR in alleviating liver fibrosis in NASH, providing initial insights into the mechanisms involved. While it offers a valuable starting point, there is potential for further exploration into the functional roles of FincoR and their specific actions in human NASH cases. Building upon the current findings to elucidate more detailed mechanistic pathways through which FincoR exerts its therapeutic effects in liver disease would elevate the research's significance and potential impact in the field.

      Strengths:

      This study stands out for its comprehensive and unbiased approach to investigating the role of FincoR, a liver-specific lncRNA, in the treatment of NASH. Key strengths include: 1) The application of advanced sequencing methods like GRO-seq and RNA-seq offered a comprehensive and unbiased view of the transcriptional changes induced by tropifexor, particularly highlighting the role of FincoR. 2) Utilizing a genetic mouse model of FXR KO and a FincoR liver-specific knockdown (FincoR-LKD) mouse model provided a controlled and relevant environment for studying NASH, allowing for precise assessment of tropifexor's therapeutic effects. 3) The inclusion of tropifexor, an FDAapproved FXR agonist, adds significant clinical relevance to the study. It bridges the gap between experimental research and potential therapeutic application, providing a direct pathway for translating these findings into real-world clinical benefits for NASH patients. 4) The study's rigorous experimental design, incorporating both negative and positive controls, ensured that the results were specifically attributable to the action of FincoR and tropifexor.

      Weaknesses:

      The study presents several notable weaknesses that could be addressed to strengthen its findings and conclusions: 1) The authors focus on FincoR, but do not extensively test other lncRNAs identified in Figure 1A. A more comprehensive approach, such as rescue experiments with these lncRNAs, would provide a better understanding of whether similar roles are played by other lncRNAs in mitigating NASH. 2) FincoR was chosen for further study primarily because it is the most upregulated lncRNA induced by GW4064. Including another GW4064-induced lncRNA as a control in functional studies would strengthen the argument for FincoR's unique role in NASH. 3) The study does not conclusively demonstrate whether FincoR is specifically expressed in hepatocytes or other liver cell types. Conducting FincoR RNA-FISH with immunofluorescent experiments or RT-PCR, using markers for different liver cell types, would clarify its expression profile. 4) Understanding the absolute copy number of FincoR is crucial. Determining whether there are sufficient copies of FincoR to function as proposed would lend more credibility to its suggested role. 5) The manuscript, although technically proficient, does not thoroughly address the relevance of these findings to human NASH. Questions like the conservation of FincoR in humans and its potential role in human NASH should be discussed.

      Reviewer #2 (Public Review):

      Summary:

      Nonalcoholic fatty liver disease (NASH), recently renamed as metabolic dysfunctionassociated steatohepatitis (MASH) is a leading cause of liver-related death. Farnesoid X receptor (FXR) is a promising drug target for treating NASH and several drugs targeting FXR are under clinical investigation for their efficacy in treating NASH. The authors intended to address whether FXR mediates its hepatic protective effects through the regulation of lncRNAs, which would provide novel insights into the pharmacological targeting of FXR for NASH treatment. The authors went from an unbiased transcriptomics profiling to identify a novel enhancer-derived lncRNA FincoR enriched in the liver and showed that the knockdown of FincoR in a murine NASH model attenuated part of the effect of tropifexor, an FXR agonist, namely inflammation and fibrosis, but not steatosis. This study provides a framework for how one can investigate the role of noncoding genes in pharmacological intervention targeting known protein-coding genes. Given that many disease-associated genetic variants are located in the non-coding regions, this study, together with others, may provide useful information for improved and individualized treatment for metabolic disorders.

      Strengths:

      The study leverages both transcriptional profile and epigenetic signatures to identify the top candidate eRNA for further study. The subsequent biochemical characterization of FincoR using FXR-KO mice combined with Gro-seq and Luciferase reporter assays convincingly demonstrates this eRNA as a FXR transcriptional target sensitive to FXR agonists. The use of in vitro culture cells and the in vivo mouse model of NASH provide multi-level evaluation of the context-dependent importance of the FincoR downstream of FXR in the regulation of functions related to liver dysfunction.

      Weaknesses:

      As discussed, future work to dissect the mechanisms by which FincoR facilitates the action of FXR and its agonists is warranted. It would be helpful if the authors could base this on the current understanding of eRNA modes of action and the observed biochemical features of FincoR to speculate potential molecular mechanisms explaining the observed functional phenotype. It is unclear if this eRNA is conserved in humans in any way, which will provide relevance to human disease. Additionally, the eRNA knockdown was achieved by deletion of an upstream region of the eRNA transcription. A more direct approach to alter eRNA levels, e.g., overexpression of FincoR in the liver would provide important data to interpret its functional regulation.

      We thank the Editor and Reviewers for their constructive comments. We believe we have addressed all of the issues (detailed below) and the revisions have greatly strengthened the manuscript.

      Reviewer 1:

      The study presents several notable weaknesses that could be addressed to strengthen its findings and conclusions:

      (1) The authors focus on FincoR, but do not extensively test other lncRNAs identified in Figure 1A. A more comprehensive approach, such as rescue experiments with these lncRNAs, would provide a better understanding of whether similar roles are played by other lncRNAs in mitigating NASH.

      (2) FincoR was chosen for further study primarily because it is the most upregulated lncRNA induced by GW4064. Including another GW4064-induced lncRNA as a control in functional studies would strengthen the argument for FincoR's unique role in NASH.

      (3) The study does not conclusively demonstrate whether FincoR is specifically expressed in hepatocytes or other liver cell types. Conducting FincoR RNA-FISH with immunofluorescent experiments or RT-PCR, using markers for different liver cell types, would clarify its expression profile.

      (4) Understanding the absolute copy number of FincoR is crucial. Determining whether there are sufficient copies of FincoR to function as proposed would lend more credibility to its suggested role.

      Response to 1 - 4): We thank Reviewer 1 for the positive comments on the strength of our work, including the open-ended approach, the novel eRNA FincoR and its strong relevance to liver disease. We also value the constructive feedback provided by the reviewer and agree that additional studies are important to fully understand the mechanisms of FincoR and the functional significance of other FXR-induced lncRNAs. In this manuscript we report the discovery and initial characterization of FincoR, as well as its potential function in FXR action in response to hammerhead agonists, but a number of interesting questions are raised. Future experiments, as suggested by reviewer, will be needed to examine the role of other FXR-induced lncRNAs, the potential role of FincoR induction by other nuclear receptors with binding sites at FincoR, whether FincoR is expressed in liver cell types in addition to hepatocytes, and the expression abundance of FincoR. These are all excellent suggestions for future experimentation which we feel are beyond the scope of the present report. For example, generating a genetic CRISPR/Cas9 of another lncRNA is not trial as it takes a significant amount of work with murine models. Also, we did not mean to exclude if other lncRNAs induced by FXR also bear functions. Technically, rescue experiment is not possible as FincoR RNA can be potentially very long (~10 kb if estimated by RNA-seq pattern in Fig.1C), and it is not feasible now to properly express it by exogenous vectors to ensure the expression levels are similar to endogenous ones. We therefore consider that these important questions are more suitable for future work to fully address. Our belief is that a comprehensive exploration of FXR-regulated lncRNAs holds the potential to unveil novel insights crucial for the development of therapies targeting NASH and other metabolic diseases. The study of FincoR is the beginning of this area of research.

      (5) The manuscript, although technically proficient, does not thoroughly address the relevance of these findings to human NASH. Questions like the conservation of FincoR in humans and its potential role in human NASH should be discussed.

      Response: These are important questions. To respond to the reviewer’s comment, new experiments are presented in our final revised manuscript in which we utilized mouse models of NAFLD/NASH and cholestatic liver injury to determine FincoR’s role in these diseases. Hepatic FincoR levels were significantly increased in mice fed with high fat diet (HFD) for 12 weeks (Supplementary Figure S1A) and in mice fed a HFD with high fructose (HFHF) in drinking water for 12 weeks (Supplementary Figure S1B). Elevated hepatic FincoR levels were also observed in mice treated with α-naphthylisothiocyanate (ANIT), a chemical inducer of liver cholestasis (Supplementary Figure S1C), and in mice with bile duct ligation (BDL), a surgical method to induce cholestatic liver injury (Supplementary Figure S1D).

      In terms of the human relevance, we have provided additional information and figures showing that there is sequence similarity between mouse FincoR and a human loci. FincoR sequence is moderately conserved between mice and humans as displayed in the UCSC genome browser (Supplementary Figure S1E). Annotation of these conserved human sequences revealed that they overlap with a functionally uncharacterized human lncRNA XR_007061585.1 (Supplementary Figure S1F). Further, we conducted qRT-PCR experiment from human patient’s RNA samples, which demonstrated that hepatic lncRNA XR_007061585.1 levels are elevated in patients with NAFLD and PBC, but not in severe NASH-fibrosis patients (Supplementary Figure S1G, H). These results demonstrate that hepatic levels of a potential human analog of FincoR are elevated in NAFLD and PBC patients, which is consistent with FincoR’s upregulation in mouse models of chronic liver disease with hepatic inflammation and liver injury. Whether human lncRNA XR_007061585.1 is entirely analogous to mouse FincoR in terms of functions and mechanisms, and whether the elevation of this human lncRNA has a role in liver disease progression or is an adaptive response to liver injury remains to be determined.

      Reviewer #2 (Recommendations For The Authors):

      (1) In the introduction Line 96, "..., while the vast majority are transcribed into ncRNAs" may not be accurate. Please refer to Pointing and Haerty Annu Rev 2022 for a related discussion.

      Response: We would like to thank the reviewer for pointing out this inaccurate information in the introduction. We have changed the content in the text, “While a significant portion of the genome was initially thought to be "junk DNA", it has been established that many non-coding regions give rise to functional non-coding RNAs.”

      (2) Figure 5: the authors should provide a clear illustration demonstrating the sequence targeted by the sgRNA in relation to the transcriptional and epigenetic profile (i.e., RNAseq and H3K27ac ChIP-seq data).

      Response: The illustration (Figure 5-figure supplement 1A, right panel) demonstrating the sequence targeted by the sgRNA has been updated as suggested by the reviewer.

      In this model, the upstream of FincoR is deleted, leading to the inhibition of FincoR transcription. Does the deleted region include FXR binding sites? If so, would the phenotype be due to the deletion of these binding sequences, rather than the decreased FincoR transcripts? Accordingly, the limitation or alternative interpretation should be discussed.

      Response: The reviewer made a good point. The deleted region includes FXR binding sites so that we cannot rule out decreased binding of FXR or decreased transcription of the region per se, in addition to the decreased levels of FincoR, to bear a role in the phenotypic changes we observed. In the final revision, we have added discussion of this alternative (6th paragraph in the revised discussion section).

      (3) Figure 6C, the images should be accompanied by quantification. It appears the FincoR-KD shows a visible difference as compared to Tropifexor-treated control mice, which does not match entirely what is written in the results.

      Response: The quantitation of Oil Red O staining has been done as suggested by the reviewer (Figure 6C). The result is consistent with the triglyceride result showing that tropifexor treatment markedly reduced neutral lipids determined by Oil Red O staining of liver sections (Figure 6C) and liver TG levels (Figure 6D) and these beneficial effects on reducing fatty liver were not altered by FincoR.

      (4) Figure 7, does AST show the same pattern as ALT? As indicated from Line 335, "tropifexor treatment reduced mRNA levels of several genes that promote fibrosis (Col1a1, Col1a2, ...)". Fig. 7D does not seem to match the description of Col1a1. Authors may need to modify the results.

      Response: AST has been measured and has the same pattern as ALT. The new data have been added to Figure 7B. Col1a1 expression has been re-measured and the results have been updated in Figure 7D.

      (5) Is FincoR level reduced in NASH conditions?

      Response: We thank the Reviewer for this question. We now added new data to examine the levels of FincoR in mouse liver disease models and also examined levels of a potential human analog of FincoR in human liver specimens from PBC, NAFLD, and NASH patients. Please see our new data and description above in the response to comment 5 by Reviewer 1 (most data now included in the new Supplementary Figure S1).

      (6) Please provide information on the conservation of FincoR (DNA and RNA) in humans. This would be important to provide the human disease relevance.

      Response: As described above in the response to comment 5 of reviewer 1, a human loci shows sequence similarity to mouse FincoR and this conserved region has an annotated uncharacterized human lncRNA. We also examined the levels of this human homolog in human diseased liver samples. Our new results demonstrate that hepatic levels of a potential human analog of FincoR are elevated in NAFLD and PBC patients, which is consistent with FincoR’s upregulation in mouse models of chronic liver disease with hepatic inflammation and liver injury. Whether human lncRNA XR_007061585.1 is entirely analogous to mouse FincoR in terms of functions and mechanisms, and whether the elevation of this human lncRNA has a role in liver disease progression or is an adaptive response to liver injury remains to be determined.

      (7) Several discussion points for the authors' consideration:

      (7.1) human-mouse conservation as alluded to in #6;

      Response: Potential human-mouse conservation is discussed with new data in the last paragraph of the Results section.

      (7.2) potential molecular mechanism involved in FincoR-regulated hepatocyte function;

      Response: We thank Reviewer for this comment. We have added more discussion as shown below: “RNA inside the cells usually associates with different RNA-binding proteins (RBPs). To predict those potential binding proteins of FincoR. Additional bioinformatic analysis identified proteins that potentially binding FincoR, including KHDRBS1, RBM38, YBX2 and YBX3 (Supplemental Table S5). These findings and potential functions of the binding proteins are discussed in the 5th paragraph of the discussion section in the final revised manuscript. Whether these predicted RBPs interact with FincoR and the underlying mechanisms will need to be investigated in future experimentation to understand the mechanisms involved in FincoR-regulated hepatocyte function.”

      (7.3) any disease-associated SNPs in the FincoR locus.

      Response: No SNPs were noted in the annotation of the human loci with sequence similarity to mouse FincoR in the NCBI genome data viewer.

      (7.4) the in vitro induction of FincoR is transient but in vivo this occurs after 12 days of drug treatment. How do the authors reconcile the differential induction patterns?

      Response: To clarify, the induction of FincoR after a single dose of GW4064 in vivo was transient, peaked within 1 h and then declined gradually (Figure 1-figure Supplement 1C). In the tropifexor treatment protocol (also in vivo), the mice were treated daily with tropifexor for 12 days so that the multiple doses maintained FincoR induction. The beneficial effect of tropifexor by inducing FincoR, therefore, accumulated over the 12 days.

      It is worthy to note that we failed to see induction of FincoR in isolated primary mouse hepatocytes treated with GW4064 in vitro. We can only detect FincoR in primary hepatocytes isolated from GW4064-treated mice liver. This may be due to the loss of key factors mediating FincoR induction in the cultured primary hepatocytes.

    1. I told him he’d have to go to the Bohemians for beer; the Norwegians didn’t have none when they threshed.

      Cather’s depiction of Bohemian and Scandinavian communities on the American frontier contributes to her pluralistic representation of America as a nation of immigrants. Her commitment to diversity is a constant presence throughout her oeuvre, namely in her 1913 novel O Pioneers!, featuring the trials of a Swedish-American family on the Nebraskan prairie. Willa Cather maintained a progressive stance on the invaluable benefit immigrants may bring to America, stating in her 1923 essay Nebraska: The End of the First Cycle , “Our lawmakers have a rooted conviction that a boy can be a better American if he speaks only one language than if he speaks two. I could name a dozen Bohemian towns in Nebraska where one used to be able to go into a bakery and buy better pastry than is to be had anywhere except in the best pastry shops of Prague or Vienna.”. While the America of the early 20th century was indeed ethnically and culturally diverse, Cather’s underrepresentation of German, Mexican and Native American communities amongst others remains a notable absence. Sources: “Nebraska: The End of the First Cycle | Willa Cather Archive.” n.d. Cather.unl.edu. Accessed March 13, 2024. https://cather.unl.edu/writings/nonfiction/nf066. Vecoli, Rudolph J. 1996. “The Significance of Immigration in the Formation of an American Identity.” The History Teacher 30 (1): 9. https://doi.org/10.2307/494217.

    1. merson admired and supported Arning’s leprosy research, although they donot seem to have collaborated directly in Hawai‘i. The men’s correspondencecontinued even after Arning returned to Germany in 1886. Both men werephysicians who pursued anthropology and Hawaiian artifact collecting asavocations, as I will discuss; both could contend for the title of first non-Native ethnographer of Hawai‘i. Arning, however, was about fifteen yearsyounger than Emerson. He trained in dermatology and the bold new field o

      Both Emerson and Arning, shared interests in anthropology and the study of Hawaiian culture despite their differences in age and primary fields of study.

    1. Paulo Freire, en su obra Pedagogía del opri-mido, cuestiona lo establecido como parte delestatuto epistemológico de la pedagogía, aldevelar que las instituciones educativas sonun lugar donde se silencia la cultura, se invi-sibilidad a los seres humanos y se impone unaforma de decir y hacer, sin considerar el con-texto socioeconómico y cultural de los edu-candos, con esto da una nueva perspectiva delas categorías esenciales y de sus relaciones,válida para entender la actividad educativacomo el objeto de los estudios pedagógicos

      Al igual que Paulo Freire debemos cuestionarnos en nuestras aulas educativas como silenciamos nuestra cultura y desvanecemos todo aquello que nos permitiría contribuir a crecer como seres humanos y no adoptar aquello que se nos impone por moda o por creer que es mejor.

    2. El resultado de la aplicación de la praxis en el actode educar colectivamente facilita poner el énfasisen las personas que enseñan y aprenden; estos setransforman mutuamente mediante el diálogo, enque el educador no solo está enseñando sino quetambién está aprendiendo, ambos logran formaruna conciencia crítica o concientizada donde seaprecia lo opresivo como un proceso que puedeser vencido

      Es importante involucrar reflexiones del docente sobre su quehacer pedagógico, cuando lo hace, porque lo hace, porque lo hace esto permitirá facilitar y garantizar la enseñanza y el aprender y esto tomando en cuenta que el dialogo es el que nos conlleva al descubrimiento de nuevas posibilidades de aprender.

    3. Buscar el porqué del analfabetismo comofenómeno multicausal, en los centros educacio-nales y los preceptos pedagógicos de la forma-ción que en ello ocurría, permitió a Freire develaren su obra Pedagogía del oprimido la esenciaexcluyente de la escuela, su intención de silenciary adoctrinar, proceso dirigido aceptar lo estable-cido como inamovible

      Importante entender las razones y el contexto de la educación en la que se desarrolla la Pedagogía del oprimido. Al leer este párrafo entiendo que la misma era opresora, el alumno era un objeto para adoctrinar con las normas del gobierno de turno o la moda de turno, segredando de las aulas no solo a los alumnos que no podian acceder a ella, sino también el criterio y la razón de cada una de las victimas de estos centros educacionales.

    1. obierno nacional, gobiernos locales, empresa privada y sociedad civil, a través de la premisa tiempo y espacio para la lectura de disfrute.

      La carga horaria en las instituciones (públicas o privadas) puede ser un impedimento para establecer estos espacios y tiempos para lectura de disfrute, incluso cuando se trata de "capacitaciones" existe una barrera burocrática para poder acceder a la propia autoformación

    2. obierno nacional, gobiernos locales, empresa privada y sociedad civil, a través de la premisa tiempo y espacio para la lectura de disfrute.

      La carga horaria en las instituciones (públicas o privadas) puede ser un impedimento para establecer estos espacios y tiempos para lectura de disfrute, incluso cuando se trata de "capacitaciones" existe una barrera burocrática para poder acceder a la propia autoformación

    3. El dispositivo o soporte más utilizado para la lectura es el celular con el 56.7%

      En la actualidad la gran mayoría de las personas posee un celular. Por lo tanto, tiene acceso a libros electrónicos y a toda la información que aparece en internet. Sin embargo, la lectura mediante este soporte se ve interrumpida por las notificaciones de las redes sociales. Adicionalmente, los individuos usan el celular más para una lectura informativa, pero es difícil ver que lean literatura. Ahora, para saber sobre un libro se prefiere leer resúmenes, videos y todo lo que nos ofrece el internet.

    4. Para el desarrollo de esta propuesta se establecerán lineamientos y trabajo coordinado con el Ministerio de Educación, Senescyt, empresas e instituciones que fomenten hábitos lectores. Además, se trabajará con todas las instituciones del Sistema Nacional de Cultura, con énfasis en los GAD, la promoción de la lectura en los espacios públicos, los barrios, casas comunales, transporte público, etc.

      Ecuador es uno de los países de la región que no contaba con una encuesta para indagar y determinar los hábitos, prácticas y consumos culturales de la población. Por lo tanto,tampoco existían estadísticas nacionales consolidadas para encaminar este tipo de propuestas. Esta encuesta sin duda, será el primer escalón a poder seguir construyendo espacios, métodos y estrategias que nos permitan construir más allá de un proyecto o plan lector, hábito de lectura desde los más pequeños pero siempre poniendo énfasis en los docentes, quienes deberíamos ser mediadores de lectura.

    5. En cuanto a la lectura en diferentes formatos, los adolescentes si leen, pero el tipo de lectura depende de los intereses de cada uno de ellos; para entretenerse, para jugar, para investigar. A algunos les gusta leer libros digitales, a otros audiolibros y a otros libros impresos. Les gusta leer textos cortos o cuentos cortos..

    6. El dispositivo o soporte más utilizado para la lectura es el celular con el 56.7%, seguido de material impreso con el 33.9%.

      Si bien es cierto que la tecnología esta evolucionando día a día, en la actualidad las personas buscan la facilidad para poder saber un libro por ejemplo ahora existen los audio-libros en donde no es necesario leer si no solo scuchar, es muy raro mirar a las personas tener un libro en sus manos y a veces es porque los libros no hay en el buscador y solo existe de manera física

    7. El 91.4% de los ecuatorianos mayores de 5 años saben leer y escribir.El 92% lee en diferentes formatos.El 76.7% lee con una frecuencia diaria.El dispositivo o soporte más utilizado para la lectura es el celular con el 56.7%, seguido de material impreso con el 33.9%.El 57.5% lee libros.En Ecuador se lee en promedio un libro completo y 2 libros incompletos al año.

      Muy importante la información que se da a conocer en este apartado con datos estadísticos nos informa acerca de los hábitos lectores en los ecuatorianos concluyendo que en Ecuador se lee un promedio de un libro completo y 2 completos al año, Adicional se manifiesta que el estado debe seguir promoviendo las practicas lectoras.

    8. El 91.4% de los ecuatorianos mayores de 5 años saben leer y escribir.El 92% lee en diferentes formatos.El 76.7% lee con una frecuencia diaria.El dispositivo o soporte más utilizado para la lectura es el celular con el 56.7%, seguido de material impreso con el 33.9%.El 57.5% lee libros.En Ecuador se lee en promedio un libro completo y 2 libros incompletos al año.

      En las cifras se refleja como se ha desarrollado la lectura en la actualidad , la mayoría de familias cuenta con un teléfono móvil con internet el cual permite acceder a diferente sitios web , relacionando con la parte educativa se puede mirar que el 57,5 lee libros pero que pasa con la otra parte para que sea un 100%.quizas esta parte que le falta la lectura lo hace pero no una lectura recreativa que permita desarrollar .