10,000 Matching Annotations
  1. Mar 2024
    1. 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.

      Estadísticas de preferencia lectora. Un indicador explora las relaciones entre escuela infantil y lectura: al 77.5 % de los encuestados los maestros les pedían comentar o exponer lecturas; a 68.8 % los motivaban a leer; y al 60.5 % les pedían leer otros libros, además de los escolares.

      Las motivaciones principales para la lectura: entretenimiento (44.1 %), trabajo/estudio (23.8 %), cultura general (20.7 %) y religiosas (10.1 %). Los temas preferentes: literatura (39.5 %), universitarios (29.5 %), autoayuda o superación personal (29.5 %), cultura general (26.5 %) y manuales, guías, recetarios (8.4 %).

      Las razones más invocadas para no leer son dos: falta de tiempo (46.7 %) y ausencia de interés, motivación o gusto por la lectura (28.1 %).

    1. En análisis recientes realizados en el contextode América Latina, coinciden en considerarlacomo ciencia dentro del campo de las humani-dades y de las ciencias sociales, que tiene comoobjetivo primordial la formación de las personaspara que, desde sus relaciones sociales y profe-sionales, puedan contribuir al desarrollo continuode la humanidad (Flórez, 1994: 33).

      En las ciencias sociales, como por ejemplo la asignatura de Cívica nos muestra esta situación de crear o de la formación de personas que sean útiles para la sociedad.

    2. El reconocimiento epistemológico del saberpedagógico, como saber experiencial, permiteconfigurar la pedagogía no solo como un con-cepto, sino como ciencia, en cuanto posee unestatuto epistemológico propio, de validez uni-versal, que le da autonomía frente a otras cien-cias para solucionar problemas de la educación.(Corredor, 2016: 30). Estos estudios permitenanalizar, de manera crítica, lo que se consideracomo los aspectos esenciales de la ciencia, eneste caso la pedagogía, y con esto cuestionar lasformas habituales y establecidas del paradigmacientificista que la sustenta, así como las prác-ticas que se valoran para conocer cómo debeentenderse y efectuarse una verdadera formaciónen una ciencia o disciplina determinada

      el siguiente aspecto se trata de reconocer el conocimiento pedagógico como conocimiento práctico ya que este nos permite construir la pedagogía no sólo como concepto, sino también como ciencia. Porque la pedagogía tiene un estatus epistemológico propio, validez universal, que le otorga autonomía sobre otras ciencias para la resolución de problemas. educación. Dicha investigación permite un análisis crítico de lo que se consideran aspectos importantes de la ciencia (en este caso la pedagogía) y las prácticas que se evalúan, así como las formas tradicionales y establecidas de paradigmas científicos que subyacen a estas preguntas. Requiere la comprensión y práctica de disciplinas específicas en una ciencia o disciplina en particular.

    3. En conclusión puedo decir que ya no estamos para oprimir a los estudiantes o verlos como personas vacias a las que debemos llenar la cabecitas con un sin numero de conocimientos, actualmente estamos para enseñar y aprender mutuamente, dando la libertad necesaria para desarrollar la práctica de reflexionar, dialogar y refutar en base a las vivencias de nuestro contexto para que así mismo ellos puedan ir formando un pensamiento mas critico y tomar decisiones. Además nos permite entender que no debemos excluir a los demás por que su cultura o condición económica sea muy distinta a la nuestra , son estas personas las que necesitan liberarse de este tipo de opresión y tienen la NECESIDAD de aprender libremente fuera de todo estereotipo.

    4. La pedagogía del oprimido, como peda-gogía humanista y liberadora, tendrá, pues,dos momentos distintos aunque interrelacio-nados. El primero, en el cual los oprimidosvan descubriendo el mundo de la opresión yse van comprometiendo, en la praxis, con sutransformación y, el segundo, en que una veztransformada la realidad opresora, esta peda-gogía deja de ser del oprimido y pasa a ser lapedagogía de los hombres en proceso de per-manente liberación”

      La pedagogía del oprimido nos permite analizar varios puntos en que la educación no se basa en que las personas son seres vacíos a los cuales se los debe llenar de conocimientos, por el contrario los dos momentos que nos invita a reflexionar Freire, nos permite comprender de mejor manera que depende de cada uno tomar la decisión de seguir como un ser oprimido o buscar una liberación permanente a través de la educación.

    5. La relación entre los educadores y los edu-candos cambian, el primero aprende del aprendiz,de la misma manera que el aprendiz aprende deleducador. Por lo tanto, cada persona a su manera,junto a otros, pueden aprender a descubrir nuevasposibilidades de la realidad de la vida, por esto laeducación se convierte en un proceso de formacióncolectiva y continua

      De acuerdo a lo mencionado en este párrafo es importante destacar que ya no se esta en la época en la que los únicos que debían aprender eran los estudiantes, y es interesante porque en la actualidad los docentes debemos entender que nosotros también aprendemos de nuestros estudiantes. en el momento que decidimos tener una relación educativa con libertad es decir que entre docente y estudiante se pueda dialogar o refutar acerca de los diferentes temas. Además todas estas acciones ayudan a formar pensamientos críticos y visualizar desde una perspectiva diferente la realidad que tiene la vida.

    6. La vida y la obra de Paulo Freire es el reflejode las circunstancias que le tocó vivir, para lapedagogía significa la ruptura de cánones y con-ceptos estereotipados que solo ve la escolariza-ción como la vía de formación y cualificación delos seres humanos.

      Mi opinión sobre esta obra de Paolo Freire y la Pedagogía del oprimido, resalta la educación y su complejidad, quedando como reflexión y comparación, en esa época las personas no contaban con acceso a la educación dejándolos a un lado de los procesos, sin embargo se apega la educación a la parte católica, en comparación un antes y un después, en la actualidad existe esta participación de la educación como un derecho que no se le niega a nadie sin discriminación o por ser parte de un grupo vulnerable .

    1. La educación postcolonial aborda la presencia delimperialismo cultural, reconociendo su legado en los currículosescolares y los supuestos occidentales sobre el conocimiento3 Original: “a lógicasubjacente da fundaçãoe do desdobramento dacivilização ocidentaldesde o Renascimentoaté hoje”.4 Original: “Acolonização falseiaas relações humanas,destrói ou esclerosaas instituições ecorrompe os homenscolonizadores ecolonizados. [...] Se oeuropeu deve aniquilarem si o colonizador,o colonizado devesuperar o colonizado”.

      Este enfoque busca desafiar las narrativas dominantes y promover una perspectiva más inclusiva y diversa en la educación, que reconozca y valore las múltiples formas de conocimiento y experiencias culturales.

    2. Epistemologías del Sur comopropuesta intelectual se centran en la lucha como resistenciacontra la dominación y la opresión, denunciando las líneasabisales de exclusión y apelando a las emergencias de saberes,incluido el uso de otras lenguas y saberes (

      La propuesta de la Epistemología del Sur implica la ruptura establecida en el ambito social, político y educativo siguiendo al parecer la línea propuesta de fines de los noventa en Brasil con la aparicion del manifiesto marginal (Ferrez) en que se desata un movimento literario dispuesto a derribar los canones establecidos. No se si la Epistemología del Sur forma parte de la expansion de estos movmientos o visceversa pero pueden estar muy relacionados a los cambios imperantes que vienen presentandose en el nuevo siglo, en el que se busca aprovechar y desterrar la exclusion de lenguas y saberes propios de la región en los procesos de educación

    3. l pensamiento abisal se constituyea partir de un “sistema de distinciones visibles e invisibles,donde lo invisible sustancia las visibles. Las distincionesinvisibles se establecen a través de líneas radicales que dividenla realidad social en dos universos distintos: el universo ‘deeste lado de la línea’, de la metrópoli, y el universo ‘del otrolado de la línea’” (SANTOS, 2007, p. 3, traducción nuestra2),del espacio colonizado. Esta división abisal producida por laepistemología imperial hace que “el otro lado de la línea” seainsignificante, residual como realidad, o incluso se produzcacomo inexistente

      El autor referenciado nos identifica el estatus claramente identificado, el poseedor de toda la validez de los concimientos y el "del otro lado" inexistente, marginal e insignificantes. Diferenciacion gravitante en el proceso de descolonizacion epistemica en el sur y de autoreconomiento como poseedores de su propio conocimento, autovalorándose y autoevaluándose lo que cognitivamente eleva el entendimento su situación actual política, educativa y social.

    4. pistemologíasdel Sur como abordaje pedagógico en la lucha contra laexclusión y el silenciamiento, por la educación hegemónicade matriz eurocéntrica y del Norte Global, de pueblos yculturas colonizadas. Asimismo, el debate cobra importanciacon la discusión de perspectivas pedagógicas decolonialesy discursos alternativos sobre la enseñanza, currículo,materiales didácticos, praxis educativa y políticas públicaseducativas o sobre discursos educativos de grupos socialmenteminorizados, en diferentes dimensiones: clase, raza, etnia,género, orientación sexual y generación.

      Las epistemologiías del Sur parten de su propio conocimiento y autopercepción en el sur global, asoman para promover la ruptura necesaria de la visión eurocentrista que viene siendo implantada en muchos ambitos entre estos la educacion; a partir de su propio conocmiento propone y debate nuevas formas para la práctica política, educativa, etc.Trata de encontrar su propia identidad entre la diversidad de grupos antes excluidos o marginados, camino en que posiblemente se cometan errores por eso es necesario que esta epistemología este bierta a debate de todos los que intervienen en todos sus procesos.

  2. www.planalto.gov.br www.planalto.gov.br
    1. As empresas de fomento comercial ou factoring

      Empresas que repassam o título que receberiam a prazo, sob a condição de receber antes porém com um desconto. "é uma operação financeira pela qual uma empresa vende seus direitos creditórios - que seriam pagos a prazo - através de títulos a um terceiro, que compra estes à vista, mas com um desconto.

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      Referee #2

      Evidence, reproducibility and clarity

      Summary

      This study highlights the role of the septin cytoskeleton in plasma membrane repair in HeLa cells perforated by the pore-forming toxin listeriolysin O (LLO). The authors performed a silencing RNA screen targeting protein-coding genes involved in endocytosis, exocytosis and intracellular trafficking. Besides the recovery of proteins that were previously identified to be part of the membrane repair machinery, they uncovered novel plasma membrane repair candidates, including septin 7 (SEPT7).

      They found that upon LLO treatment, septins redistribute from actin stress fibers to the cell surface where they form knobs and loops together with F-actin, Myosin-IIA and Annexin A2 (ANXA2). Using super resolution microscopy and 3D reconstruction, they showed that these structures often protruding from the cell surface are formed by septins and F-actin that are organized in intertwined filaments associated with Annexin A2, and that they are functionally correlated with plasma membrane repair efficiency. Silencing SEPT7 further revealed that the remodeling of the repair protein ANXA2 at the cell surface is greatly decreased in LLO-injured cells, whereas the down regulation of ANXA2 had no impact on the arrangement of septins and F-actin into knobs and loops. Altogether, their results evidenced that the septin cytoskeleton triggers the organization of membrane domains containing the actomyosin cytoskeleton and ANXA2, that are essential for the repair to occur.

      Major comments:

      • The authors show that silencing SEPT6 or SEPT7, but not SEPT2 or SEPT9, perturbed plasma membrane repair of LLO-injured cells. The authors explain this result by indicating that the reduced expression of SEPT7 and SEPT6 (according to the siRNA), but not that of SEPT2 results in a reduced expression of septins from other groups. This could have been an explanation but, in Fig. S2B, downregulating SEPT2 clearly seem to impact the expression of SEPT6 and SEPT7 (except for siRNA#3) once normalized with the loading control tubulin. Moreover, it is well accepted in the literature and has been observed in many cell types, including HeLa cells, that knocking down a septin from one group (with sometimes the exception of septins of Group 3) induces the downregulation of septins of the other groups, and that it consistently results in the loss of septin filaments. Therefore, the fact that silencing SEPT2 does not perturb plasma membrane repair is quite surprising. This could suggest that SEPT6 and SEPT7, independently of their filament organization, play a role in membrane repair after LLO treatment. Nevertheless, the SEPT2 staining to study the fate of septin filaments following LLO exposure indicated that it is the redistribution of septin filaments that is crucial in this repair process. Interestingly, BORG proteins which are involved in the association of septin filaments to the actin cytoskeleton in interphase cells bind to the SEPT6/SEPT7 coiled-coil region of septin polymers. Could these proteins be involved, knowing that they are Cdc42 effector proteins, and that links exist between Cdc42 activation and Ca2+ entry? OPTIONAL: silencing BORG proteins (BORG2 for example) and studying septin and F-actin remodeling following LLO exposure could help the authors to understand the reason of such a redistribution.
      • What about the terms "knob" and "loop": Are they structurally related to the "specks" described in other papers? Or are they new structures that no one observed before? Nobody has never looked at septins in this repair process before, but actin has long been described to be involved.
      • It seems that knobs are formed before loops take over. This would deserve further investigation. Is that a reality? Or are they two independent structures? OPTIONAL: it would be interesting to do time-lapse video microscopy to follow the fate of a knob. Related to the previous point: why to show 3 sets of images in the LLO condition in Fig. 2A? Does the top b-panel represent the knob stage? Where there are still many stress fibers indicating that septins have not yet fully redistributed? And when septins are fully dissociated from actin cables, which are then lost, loops are forming (middle c-panel) and then increase in size (bottom d-panel)?
      • Even though, some information is given in the discussion section, it would be helpful to mention in the introduction section the different pathways that cells activate to repair plasma membrane defects, and to precise which one(s) has(ve) already been described in the literature to be switched on in response to the LLO toxin.
      • Some experiments are not rigorous enough: Sometimes, they have not been repeated, as exemplified in Fig. 7B. Count less cells but repeat the experiment at least three times. Sometimes, one condition is missing, as in Fig. 6C. Where is the DMSO condition? What about the statistics? Fig. 6A: In the calcium free condition, it seems that the two cells that are illustrated depict a telophase. The subcellular organization is obviously different at the end of cell division. Show only one interphase cell as in the top panels. Fig. 6B and C: It is mentioned in the figure legend: "Cells were treated as indicated in (A) and (D)". But the "C" condition is not mentioned anywhere: Does "C" stand for no DMSO or FCF treatment, in the presence of calcium, but under LLO treatment? Likewise, it would be very helpful to indicate in each figure panel whether cells have been treated with LLO or FCF. Please help the reader. Fig. 7A: Whatever SEPT7 is expressed or downregulated, the actin stress fibers are still present. If these cells were not well transfected, replace the images.
      • Concerning the FCF experiments: The FCF cytokinin has been used by many authors to perturb septin dynamics. It induces the stabilization of septin polymers, thus promoting the formation of thick ectopic fibers. It is a potent inducer of septin polymerization and acts as a stabilizer. Fig. 6D: In the Ctr condition, a DMSO condition is needed to visualize the impact of FCF on septin filaments. Does FCF stabilize septins and induce the formation of thick filaments? The SEPT2 image in the FCF condition without LLO is of bad quality (see above remark). Also in Fig. 6D (FCF condition without LLO), the F-actin staining revealed that there are no stress fibers!!??? Usually, the more septins are associated with actin, the thicker stress fibers you get, since septins stabilize actin cables. FCF treatment often induces thick ectopic septin filaments that are not associated with stress fibers (which are therefore lost). Was it the case in all FCF-treated cells? Does FCF treatment really mimic what happens physiologically in the cell? Many off-target effects have been observed with this molecule in non-plant cells.
      • The image quality in Figs 3A and B, and 6A and D needs to be improved regarding the septin staining. In control conditions, septin filaments cannot be clearly distinguished.
      • Fig. 3B: It seems that ANXA2 is overexpressed in LLO-injured cells. Its accumulation level between both conditions should be compared by immunoblot. ANXA2 is indeed recovered on loops, but it is difficult to consider whether it is a redistribution.
      • Fig. 7D: Compared to the control condition (we have to refer to Fig. S5D), ANXA2 again seems to be overexpressed under LLO treatment. To affirm that ANXA2 remodeling in LLO-injured cells requires the formation of septin/F-actin knobs and loops, data in Fig. 7D must be quantified.
      • Fig. 6 (B-D): In panel B, there is a significant difference between the "C" and "FCF" conditions regarding the number of knobs + loops per cell. Where are the images corresponding to the "C" condition?

      Minor comments:

      • Fig. 2A: Report the white squares (selected enlarged areas) in all panels (SEPT2 and overlay). In panels b, do not place an arrowhead where we are supposed to observe an enlarged area. Also, from panels b, it would be worth showing an enlarged area including a knob. Show enlarged areas also from panels d.
      • Fig. 3B'i: Septins are not on stress fibers. Select a transfected cell where septins still coalign with actin fibers, not a cell that was impaired by the transfection.
      • Fig. 3C: Add the time point "0min". What was the % of colocalization before LLO treatment? and in DMSO condition? What about ALIX at 5 and 10min? Again, it's only one experiment.
      • Figs 4 and 5: Very nice images but obtained following FCF exposure. Hopefully FCF would not have induced an aberrant organization!
      • The "Ctr" abbreviation is often used, in different conditions, and may be confusing. Precise in the figure (not in the figure legend) whether it is siRNA ("Ctr siRNA"). Mention "DMSO" for the controls of your drugs (like in Figs S4 and S5).
      • Fig. S4C: How is this figure different or does it provide additional information compared to Fig. 2C?
      • Fig. S5D: It is hard to know that the ANXA2 siRNA worked, since no difference of staining between the Ctr and the transfected cells can be observed. Were these cells really transfected? It would have been helpful to use fluorescent siRNAs. The same applies to Fig. S5C: Silencing SEPT7 supposedly greatly reduces the level of expression of all septins. The SEPT2 staining is still high, and many actin stress fibers are still observable (whereas the loss of septin filaments results in the loss of actin stress fibers, as observed by many authors, including in HeLa cells). Same remark for Fig. S6, regarding the SEPT7 silencing in the Ctr condition (no LLO). No impact on stress fibers! Are these cells transfected? The authors themselves mention that sometimes cells are less effectively silenced (like in Fig. 7A, B). Why not to show cells effectively silenced!!
      • In the abstract, it is specified that SEPT7 also plays a role in membrane repair after mechanical wounding. Based only on one type of experiment (SEPT7 silencing, Fig. 1H), this statement should only be mentioned in the text or used to discuss the putative repair mechanisms that septins are involved in, but not stated in the abstract as a main conclusion.

      Significance

      Strengths:

      Despite septins have been involved in endocytosis, exocytosis, membrane protrusions, cell junction integrity or actomyosin constriction at cytokinesis, the involvement of the septin cytoskeleton in the plasma membrane repair machinery has, to my knowledge, never been reported before. The authors not only showed that septins are present in specific membrane protrusions (knobs and loops) but also evidenced that septin filaments trigger the formation of these plasma membrane repair domains by recruiting F-actin and ANXA2, essential for the repair to occur. The novelty of this study has therefore to be acknowledged, and these data will benefit the scientific community, and the septin community in particular.

      This is a descriptive paper that nevertheless clearly shows, by different means, the reorganization of the septin cytoskeleton in LLO-injured cells. The use of high-resolution microscopy coupled to 3D reconstruction which enables to easily appreciate the organization of septins, F-actin and ANXA2 in the knobs and loops is a true strength of the paper.

      Limitations:

      The authors mention in the abstract that septins act as scaffolds to recruit contractile actin fibers and ANXA2. Biochemical experiments such as co-immunoprecipitations could strengthen this notion. The molecular mechanism by which septins are involved in this repair process has not been addressed at all in the paper. Even though the silencing RNA screen highlighted several proteins involved in known membrane repair mechanisms, the authors just presented a few data concerning ALIX, a component of the ESCRT-III machinery. A % of colocalization of SEPT2 and SEPT7 with ALIX is reported in Fig. 3C but this experiment has only been done once (n=1) and only following 15-min exposure to LLO. Is that too late? Immunofluorescence images of SEPT2 and ALIX with or without LLO (15min) are also provided in Fig. S5A but no quantification is reported. Is it sufficient to say that the ESCRT machinery is not involved?

      My field of expertise:

      Cytoskeleton, Septin, Actin, Microtubule, Signaling pathways

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      Reply to the reviewers

      General Statements

      We are grateful to the reviewers for reviewing our manuscript. In general, the reviewers agree that our method presents a new approach of Nanopore direct RNA-seq that is not limited to the standard use of only the adenylated fraction of RNAs within a sample but they have also requested more evidence about the effectiveness and usefulness of this approach. Reviewer 1 notes that NERD-seq "extends nanopore direct RNA-Sequencing to beyond the poly(A) fraction." Reviewer 2 notes that "This manuscript has the potential of having major significance to researchers in the field of transcriptomics". At the same time Reviewer 1 remarks that, "the authors need to expand more on why this is useful, and what scenarios this would be used in" and need "to demonstrate that NERD-Seq is more than an incremental improvement to existing approaches". Reviewer 2 notes that "This technique has great potential, as ONT direct RNA sequencing can be used to detect RNA modifications... There are however some issues that need to be addressed before the manuscript is suitable to publication" and agrees with Reviewer 1 that the authors need to demonstrate "that their newly sequencing techniques could indeed improve RNA detection beyond the current techniques." We are grateful to the reviewers for these comments, and we fully agree that the manuscript in its initially submitted form falls "short from providing strong arguments supporting the fidelity, accuracy and coverage of the new technique." and that more "proof of the increased accuracy or utility of the new technique" was needed.

      We attach a substantially revised and expanded version of the manuscript that includes additional data needed to ensure the methodology is replicable and further supports the rationale why NERD-seq is a useful addition to the current direct RNA sequencing methodology repertoire. We now provide:

      • the repetition of all performed NERD-seq runs with a new enzyme (commercially available), as the one used in our initial study (Omniamp polymerase) is not anymore commercially available

      • 6 revised main figure panels based on the new sequencing runs and a new main figure (Fig.7),

      • 20 new supplementary figures, and

      • 1 new supplementary table (Suppl. Tables 1),

      that correspond to the points raised by the reviewers. We have also revised the main text accordingly.

      Please find below the reviewers 'comments and a detailed point by point response to these comments. A document with the changes from the initially submitted manuscript being highlighted is attached at the end of this response.

      Point-by-point description of the revisions

      Reviewer 1

      *------------------------------------------------------------------------------ *

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

      • *

      ***Summary:** *

      • *

      This reviewer generally remarks that: "Saville et al detail a new method, NERD-Seq, which extends nanopore direct RNA-Sequencing to beyond the poly(A) fraction. In principle, this allows the capture of additional RNA types in a single sequencing reaction, albeit at the expense of sequencing depth. However, the authors need to expand more on why this is useful, and what scenarios this would be used in. The rationale for many of their experimental choices are not explained/contextualized appropriately. The manuscript also suffers from excessive jargon and grammatical errors."

      • *

      We appreciate these comments made by the reviewer. We now expand more on why and how NERD-seq is useful, and what scenarios this could be used in. In particular:

      In the introduction, we now denote that a significant number of the most well described RNA modification positions are located in classes of RNAs such as tRNAs, snoRNAs and other ncRNAs like 7SK RNA. In the results section, we build on the second reviewer's suggestion that "This technique has great potential, as ONT direct RNA sequencing can be used to detect RNA modifications...", and we first show in revised Figures 3-5 that the standard approach misses the above classes of RNAs. Subsequently, in two new figures (Fig. 7 and Suppl.Fig. S23) we present an example of the ability of NERD-seq to decipher known RNA modifications in a well-studied ncRNA, 7SK, compared with the inability of the standard approach to do so. Widely studied RNAs such as 7SK have the potential and thus often serve as controls for known positions of certain RNA modifications when validating them for novel positions in other RNAs. This however means that the application of the standard approach, which is not able to detect RNAs and thus their modifications for RNAs such as 7SK, makes it difficult to use them as controls. In other words, the ability to perform genome wide studies of RNA modifications using the direct RNA-seq approach relies on the ability to be able to confirm at the same time these findings in already known control positions located in the above classes of RNAs. If these known controls such as short ncRNAs are missing, as we show that it is the case with standard RNA-seq, it is difficult to perform such genome wide epitranscriptome studies. Thus, the usefulness of our approach is not only that it can sequence certain classes of shorter RNAs beyond mRNAs, but that it can do this without affecting the ability to study mRNAs simultaneously or use targeted sequencing adapters. This is now discussed in the text. We have also tried to avoid the excessive use of jargon language and correct any grammatical errors.

      *------------------------------------------------------------------------------ *

      ***Major comments:** *

      • *

      Point 1. The reviewer mentions:* "To my understanding, the primary purpose of NERD-Seq is to allow the sequencing of the non-adenylated fraction of RNAs within sample with a size filter step designed to exclude ncRNAs larger than ~200 nt. While this allow for subsequent polyadenylation of the small fraction, it remains quite likely that larger non-adenylated non-rRNAs are being missed by the protocol. It is also not clear why NERD-Seq should be considered the optimal strategy. The authors should show that they have considered/evaluated other strategies such as: *

      *- Depletion/Seperation of the poly(A) fraction prior to size selection performed on non-adenylated fraction. *

      - Targeted degradation of the rRNA fraction using rRNA depletion kits."

      • *

      We thank the reviewer for this comment. The primary purpose of NERD-seq is not only to allow the sequencing of the non-adenylated fraction of shorter RNAs but to do this while maintaining the ability to sequence longer polyadenylated RNAs. In particular, we are not sequencing only the short RNA fraction but also the longer RNA fraction of naturally polyadenylated RNAs. This includes both mRNAs and ncRNAs that are polyadenylated. We apologize that this may have not be presented clearly in our initial text, and we have now revised the respective results part (page 8, lines 13-14 and 30-31). As mentioned below, we now also provide evidence that our approach does not affect the ability to efficiently sequence mRNAs and decipher effectively their isoforms (new Suppl. Fig. S19). Only large non poly-A ncRNAs still evade our detection. Now, we discuss this limitation in the last paragraph of the discussion section (page 19, lines 12-20). We have now also evaluated other strategies such as those mentioned by the reviewer (depletion of rRNA, size selection using magnetic beads, different enzymes) and in the new Suppl. Figure S5 we show that they were suboptimal in providing sufficient reads that pass the quality thresholds in base calling compared to our NERD-seq approach.

      • *

      To sum up, we certainly don't claim to be able to capture longer ncRNAs, due to their lack of polyadenylated tails. We show though that while the ability to capture simultaneously all reads under the current Nanopore sequencing protocols may be unattainable, the NERD-seq methodology demonstrates a useful addition to the Nanopore sequencing repertoire due to its ability, in addition to polyadenylated transcripts, to simultaneously capture multiple classes of short ncRNAs, hitherto until now only achievable one transcript at a time with custom adaptor ligation.

      Point 2. The reviewer mentions that "Related to this, the authors note that NERD-Seq is designed to allow the sequencing of both adenylated and (short) non-adenylated fractions of RNAs within a study. What is the actual value of this versus, say, simply targeting the short non-adenylated fraction directly?"

      Please see our response to the general comment by this reviewer and the new figures Fig. 7 and Suppl. Fig. S23 and the completely new results section at pages 15 and 16 about examples on how NERD-seq expands the study of epitranscriptomic signatures to additional RNA classes while maintaining the ability to efficiently assess the protein coding transcriptome (new Suppl. Fig. S19).

      Point 3. The reviewer notes that "The manuscript in general is written in a somewhat subversive style, seemingly focused on highlighting the 'failings' of the standard ONT protocol. This is somewhat disingenuous as these are not 'failings' per se given the design objective of the standard DRS protocol (i.e. to capture and sequence the poly(A) fraction of RNAs) works well. The authors would be better off highlighting the situations (i.e. study questions) where NERD-Seq would provide a measurable benefit over the standard DRS strategy."

      • *

      We apologize if this was indicated in our initial submission, as this was not our intention. We now focus on highlighting what NERD-seq can do, and this is reflected in the changes we have made in the introduction and discussion section.

      Point 4. The reviewer asks "The authors state that 1.5ug total RNA is used as input for NERD-Seq but how much input (poly-A RNA) actually goes into the short- and long-fraction parts of the DRS protocol? This is important to know. "

      We have now included data in the manuscript for polyadenylation signals in the reads themselves (new Suppl. Fig S5F) and view it as a useful addition to the manuscript as it seems to show there is little difference in the relationship of length of transcript and polyadenylation tail length between the two methods.

      RNA RIN values differ across samples so within different samples the portions of poly-A RNA, non poly-A RNA and former poly-A RNA that has lost the poly-A due to degradation may also vary. This however has not been shown to affect the reproducibility of the standard direct RNA-seq methodology, so it should not affect also that of NERD-seq. Nevertheless, we searched the literature for a well characterized methodology for quantifying this further and found little on poly(A) specific quantification approaches that we could use. In fact, poly(A) selection has also been shown to have variable efficiency and could thus produce inaccurate measurements that would make it difficult for us to assess explicitly the exact portions of poly-A vs non poly-A portions. Thus, we feel that in the absence of a well characterized methodology to make these quantifications, developing a new one may have been beyond the scope of this manuscript.

      Point 5. The reviewer recommends: "The authors show that NERD-Seq performs well on a tissue that is generally enriched in non-coding RNA activity but without the inclusion of biology replicates or tissue samples from other sources, it is impossible to assess (1) the reproducibility/robustness of the methodology and (2) whether NERD-Seq would produce useable data from other tissues with lower non-coding RNA activity. These experiments are required."

      • *

      We thank the reviewer for this suggestion and we have now included an additional biological replicate for the mouse tissue and data from another tissue in a separate organism (5-person pool source human cerebral cortex RNA).

      Point 6. The reviewer notes: "Several figures are poorly explained. For instance, Does Figure 2A show data only from the short RNA fraction? If not then this suggests incredibly high levels of mRNA degradation in the 'standard' ONT fraction - far beyond what is seen in other studies. The legends for all figures should be far more specific and detailed."

      • *

      We have now replaced figure 2A with a different mapping strategy and a whole sample assessment of mapped reads lengths. We have also edited the figure legends to include more information.

      The reviewer made also the following comments:

      Minor comments:

      • *

      ": Please refrain from using 'next-generation' in a sequencing context (abstract, introduction). Having a 'new' next-generation sequencing is confusing in regard to the old 'next generation' sequencing."

      • *

      The instances mentioned have been removed as per the reviewer's suggestion.

      "Introduction should acknowledge that targeted sequencing of (individual) non-adenylated RNAs is possible (i.e. there is an ONT protocol for this)."

      • *

      We now include mention of this in the introduction, results and discussion.

      "Several figure elements not referenced in the text appropriately (e.g. red bars in Figure 2A)."

      • *

      We have now addressed this and thank the reviewer for making us aware of this.

      "The authors mention profiling of the epitranscriptome several times in the introduction and discussion but do not include any work geared toward looking for RNA modifications. Indeed it is entirely unclear whether NERD-Seq produces the depth of sequencing (on non-adenylated RNAs) required for current RNA modification detection tools."

      • *

      We have now included a new main figure (Fig. 7) and a new supplementary figure (Suppl. Fig. S23) which profile elements of the epitranscriptome and show that indeed NERD-seq produces the depth of sequencing necessary for RNA modification detection.

      Reviewer 1's summary:

      • *

      "NERD-Seq presents a modified method for DRS of both short non-adenylated and the standard adenylated fraction of RNAs within a sample. This utility of this approach appears rather niche and it is hard to determine situations in which this approach would be generally useful versus many of the existing (Illumina-based) approaches. The burden to demonstrate that NERD-Seq is more than an incremental improvement to existing approaches lies with the authors."

      • *

      We appreciate the reviewer's comments. While we agree with them that for various applications (such as differential gene expression, quantification of lowly expressed genes) "the existing (Illumina-based) approaches" Illumina RNA-seq or short-RNA-seq would be more appropriate due to higher sequence yields, the main advantage of nanopore direct RNA-seq is the ability to identify RNA modifications directly at the same time (see new Figs 7 and S23). While we also agree that the field of high throughput sequencing epitranscriptomics is quite nascent, it is quickly gaining interest. Based on the reviewer's suggestions we believe that we have now modified the manuscript substantially to provide justification for NERD-seq's feasibility as a methodology to capture multiple classes of ncRNAs for the study of their sequence, quantity and their epitranscriptomic signatures.

      We would also like to note that even as a BioRxiv preprint, our manuscript has received already a number of citations, including from an article published in Nature Biotechnology and feel this demonstrates interest in NERD-seq from the scientific community.



      Reviewer 2

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

      • *

      This reviewer generally remarks that "In this manuscript Saville et al. present NERD-seq, a novel method to enrich and directly sequence non-coding RNA using the Oxford Nanopore Technology (ONT). The technique is based on the addition of a poly-A tail to small non-coding RNAs which enables their sequencing by a conventional ONT direct RNA-seq protocol using a poly(T)-tethering adaptor. This technique has great potential, as ONT direct RNA sequencing can be used to detect RNA modifications. Furthermore, non-coding RNAs are known to harbor a lot of these modifications and that they are important to their function. In addition, non-coding RNAs aren't generally poly-adenylated and therefore are underrepresented when using standard ONT direct RNA-seq. The authors have shown that using NERD-seq, they are able to significantly improve the number of reads on several subsets of non-coding RNAs : tRNAs, snoRNAs, snRNAs, scRNAs and rRFs. There are however some issues that need to be addressed before the manuscript is suitable to publication."

      • *

      We thank the reviewer for their encouraging comments.

      Major comments:

      • *

      Point 1. The reviewer recommends that "Data on RNA modifications present in the sequenced non-coding RNA would greatly improve the impact of the manuscript, as the method is presented as read tool to study RNA modifications. If the authors can't include these data, they should at least explain why in the discussion section."

      • *

      We have now included a new main figure (Fig.7) and a supplemental figure (Suppl. Fig. S23) which show the ability of NERD-seq to identify previously described RNA modifications and its superiority in the case of non-coding RNAs such as 7SK. We thank the reviewer for this recommendation that significantly improved our manuscript better revealing the rationale and impact of our approach.

      Point 2. The reviewer remarks that "The authors did not discuss possible biases of their method. For example, is the poly-A tail ligation efficiency affected by sequence and or structural differences between RNA? Is there detectable differences in the efficiency of sequencing small RNA with structured 3'end when compared to mRNA? Are the proportions of reads obtained per non-coding RNA sub-category and RNA rank supported by other biochemical data (e.g. Northern blots, primer extension, RT-qPCR?"

      • *

      We have included commentary in the discussion on these biases (page 19, lines 7-11). We also include a new supplementary figure (Suppl. Fig. S5F) regarding polyadenylation in which we see similar transcript length to polyadenylation tail length dynamics between the two methodologies.

      Point 3. The reviewer notes that "It is essential to include external size and sequence markers spike-in to directly evaluate the quality and fidelity of the newly develop sequencing technique."

      • *

      We have now repeated the sequencing, including sequencing with the well described RNA sequins mix B. We include a new supplementary figure with this data (Suppl. Fig. S10) that shows that NERD-seq does not differ from the standard approach regarding its ability to effectively evaluate the quantity and complexity of the transcripts present.

      Point 4. The reviewer mentions that "The author compared NERD-seq to ONT standard direct RNA-seq but did not compare it with other methods that are currently used for non-coding RNA sequencing (e.g. Illumina based sequencing, TGIRTseq). There is a need for side by side comparison at least by using data available in the literature if not experimentally."

      • *

      We now include a comparison with Illumina sequencing data for both long and short fractions from each biological replicate (Suppl.Figs S12-15,17,19 and 21). This data shows that NERD-seq combines the advantages of both standard and short RNA-seq with Illumina, enriching both long and short RNAs, while simultaneously as mentioned above, offering the benefits of direct RNA-seq. We feel this also demonstrates the utility of the unique chemistry of Nanopore sequencing where fragmenting of long RNAs is not required for sequencing, allowing the combination of long RNAs and short RNAs in the same library to reproduce what is essentially enriched in short RNA libraries as well as poly(A) sequencing libraries. Since the enzyme included in our initial submission is not anymore widely accessible, we also tested a series of other enzymes, including the commercial replacement for omniamp (the originally used enzyme), lavalamp, and other small tweaks to the library methodology, until finding the GSP SSD2.0 enzyme to be the most suitable for our research goals. The summary of our findings is in Figure S5. Initially, we considered TGIRT as a potential enzyme for the sequencing reaction because of its use for sequencing snoRNAs and other highly structured RNAs but because of its strand switching properties, we felt it would be poorly suited for a nanopore direct RNA sequencing approach.

      The reviewer made also the following comments/suggestions:

      Minor comments

      • *

      "Page 5 line 3, NERD-seq is misspelled."

      • *

      This is now fixed.

      "Throughout this section µL and µg are written as uL and ug."

      • *

      This is now fixed.

      "Several temperatures are missing the o symbol between the number and C."

      • *

      This is now fixed.

      Final comments:

      • *

      "This manuscript has the potential of having major significance to researchers in the field of transcriptomics if the author demonstrated that their newly sequencing techniques could indeed improve RNA detection beyond the current techniques. Unfortunately, the manuscript only show the capacity of the technique to detect non-coding RNA but fall short from providing strong arguments supporting the fidelity, accuracy and coverage of the new technique. The use of Nanopore sequencing is not unique and was used in the past for sequencing non-coding RNA. What is needed now is a proof of the increased accuracy or utility of the new technique to justify yet another publication about Nanopore sequencing paper. The manuscript would potentially be of interest to researcher working on different type of non-coding RNA and transcriptomics.* *

      • *

      I am in the field of non-coding RNA sequencing and functional analysis and very familiar with this approach."

      • *

      We thank the reviewer again for their encouraging comments and valid concerns. We agree that the initial manuscript fell short of providing evidence of its utility as an addition to the Nanopore sequencing repertoire. We hope the additional data we provide (rerunning with an additional enzyme, use of replicates, use of standard spike in controls, testing an additional organism and tissue, testing and comparing different enzymes and other sequencing platforms) provide the necessary assurances about reproducibility and accuracy, while the new data concerning identification of RNA modifications and detection of important RNA classes missed by the standard protocol provides the necessary assurances about the utility of our approach.

    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

      In this manuscript Saville et al. present NERD-seq, a novel method to enrich and directly sequence non-coding RNA using the Oxford Nanopore Technology (ONT). The technique is based on the addition of a poly-A tail to small non-coding RNAs which enables their sequencing by a conventional ONT direct RNA-seq protocol using a poly(T)-tethering adaptor. This technique has great potential, as ONT direct RNA sequencing can be used to detect RNA modifications. Furthermore, non-coding RNAs are known to harbor a lot of these modifications and that they are important to their function. In addition, non-coding RNAs aren't generally poly-adenylated and therefore are underrepresented when using standard ONT direct RNA-seq. The authors have shown that using NERD-seq, they are able to significantly improve the number of reads on several subsets of non-coding RNAs : tRNAs, snoRNAs, snRNAs, scRNAs and rRFs. There are however some issues that need to be addressed before the manuscript is suitable to publication.

      Major Comments:

      • Data on RNA modifications present in the sequenced non-coding RNA would greatly improve the impact of the manuscript, as the method is presented as read tool to study RNA modifications. If the authors can't include these data, they should at least explain why in the discussion section.

      • The authors did not discuss possible biases of their method. For example, is the poly-A tail ligation efficiency affected by sequence and or structural differences between RNA? Is there detectable differences in the efficiency of sequencing small RNA with structured 3'end when compared to mRNA? Are the proportions of reads obtained per non-coding RNA sub-category and RNA rank supported by other biochemical data (e.g. Northern blots, primer extension, RT-qPCR?

      • It is essential to include external size and sequence markers spike-in to directly evaluate the quality and fidelity of the newly develop sequencing technique.

      • The author compared NERD-seq to ONT standard direct RNA-seq but did not compare it with other methods that are currently used for non-coding RNA sequencing (e.g. Illumina based sequencing, TGIRTseq). There is a need for side by side comparison at least by using data available in the literature if not experimentally.

      Minor Comments:

      • Page 5 line 3, NERD-seq is misspelled.

      • Throughout this section µL and µg are written as uL and ug.

      • Several temperatures are missing the o symbol between the number and C.

      We recommend that all these issues should be addressed before publication.

      Significance

      This manuscript has the potential of having major significance to researchers in the field of transcriptomics if the author demonstrated that their newly sequencing techniques could indeed improve RNA detection beyond the current techniques. Unfortunately, the manuscript only show the capacity of the technique to detect non-coding RNA but fall short from providing strong arguments supporting the fidelity, accuracy and coverage of the new technique. The use of Nanopore sequencing is not unique and was used in the past for sequencing non-coding RNA. What is needed now is a proof of the increased accuracy or utility of the new technique to justify yet another publication about Nanopore sequencing paper. The manuscript would potentially be of interest to researcher working on different type of non-coding RNA and transcriptomics.

      I am in the field of non-coding RNA sequencing and functional analysis and very familiar with this approach.

    1. Las figuras de Venus, un término general para varias estatuillas prehistóricas femeninas retratadas con atributos físicos similares, eran muy populares en ese momento. Estas figuras fueron talladas en piedra blanda (como esteatita, calcita o piedra caliza), hueso o marfil, o formadas de arcilla y cocidas.

      tipos de figuras en las pinturas repestres forma del arte en la edad de pierda ._.

    1. Cuando la integridad física, psicológica o sexual de las niñas, niños y adolescentesestuviere amenazada o hubiere sido afectada, sin perjuicio de la obligación de denun-ciar por parte de quien en la comunidad educativa tuviere conocimiento del hechocuyas características hagan presumir la existencia de amenaza o afectación, la JuntaDistrital Intercultural de Resolución de Conflictos denunciará ante la autoridad judicialrespectiva

      "La existencia de amenaza o afectación" implica que el sistema educativo este en capacidad de detectar presuntos casos de amenaza de la integridad y pueda intervenir a un nivel complejo como el judicial lo que puede generar situaciones complejas para los docentes en caso de no tener el soporte institucional pertinente

    2. Por su parte, el principio de laicidad o laicismo estáconsagrado en el artículo 28 de la Constitución, así como en el artículo 2, literal “y” de laLOEI,

      Es muy importante ser enfática al mencionar la ruptura de desigualdades sociales, dando oportunidad de acceso a los Sistemas Educativos a todo tipo de personas, especialmente a los más desprotegidos. De igual manera, la Constitución de la Re­pública del Ecuador, marcó un hito al considerar que la Educación es “un derecho de las personas a lo largo de su vida y un deber ineludible e inexcusable.

    3. En nuestro país no existían reglas claras sobre la honestidad académicaen el ámbito escolar; como consecuencia, prácticas tales como la copia yel plagio se extendieron en el sistema educativo y en buena parte quedabanimpunes. Partiendo de que presentar como propios los productos académicoso intelectuales que no son el resultado del esfuerzo personal no es ético —yciertamente no promueve el aprendizaje—, el Reglamento a la LOEI exige elcumplimiento de normas internacionales de honestidad académica por parte detodos los miembros de la comunidad educativa y establece severas sancionespara quienes infrinjan estas normas.

      La integridad académica contribuye a construir una comunidad educativa justa, honesta y responsable. Es un medio para sumar valor a tu institución educativa, ya que sirve de garante de la verdadera valía de los estudiantes que obtienen los títulos. Si bien es cierto con el uso de las nuevas tecnologías se han perfeccionado ciertas prácticas deshonestas como el plagio o la usurpación de identidad, en paralelo a esto se han desarrollado nuevas herramientas para poder prevenirlas y detectarlas. A su vez introduce cambios para lleva a una buena práctica académica fomentando el valor de la honestidad académica.

    4. la interculturalidad propone un enfoque educativo inclusivo que, partiendo de la valo-ración de la diversidad cultural y del respeto a todas las culturas, busca incrementar laequidad educativa, superar el racismo, la discriminación y la exclusión, y favorecer lacomunicación entre los miembros de las diferentes culturas”. El rescate del patrimo-nio social y cultural que caracteriza a cada pueblo y nación permitirá la cohesión deuna sociedad enfocada al cumplimiento de metas de desarrollo comunes

      Una persona interculturalmente competente dispone del conocimiento acerca de su propia cultura y de otras culturas diferentes. por lo mismo es indispensable para la competencia intercultural. La persona competente es capaz de identificar obstáculos de comunicación en la interacción y puede expresarlos en el medio que se encuentre sin rasgos de racismo o discriminación.

    5. En el artículo 140 del Reglamento se detallan algunas de estas, como laprohibición de que se exija a los estudiantes o a sus familias el pago de cualquier contribu-ción económica que no esté expresamente autorizada por el Ministerio de Educación, o elpago de mensualidades adelantadas por concepto de pensiones o matrículas. Tambiénse establece que, de acuerdo con el principio de inclusión educativa, los establecimientoseducativos particulares y fiscomisionales no podrán cobrar valores adicionales a ningún es-tudiante en atención a sus necesidades educativas especiales. Del mismo modo se prohíbeque estos establecimientos diferencien la calidad del servicio ofrecido a sus estudiantes enfunción de los valores que cobran.

      Es interesante el articulo 140 del reglamento, ¿cómo determina el Ministerio de Educación la autorización de rifas o contribuciones a eventos religiosos en colegios fiscomisionales? ¿qué proceso se aplica?

    6. el nuevomarco legal fortalece la protección de niños y adolescentes al garantizarles su derecho arecibir el servicio educativo de manera continua, sin interrupciones de carácter político,partidista, gremial o de cualquier otra índole, que tanto daño han hecho, sobre todo a lacalidad de la educación pública.

      La razón por la que fue necesario un cambio radical es la protección de niñas y niños en cuanto a la continuidad y libre acceso al que es ahora un derecho, la educación.

    7. Garantizar la alfabetización digital y el uso de las tecnologías de la informacióny comunicación en el proceso educativo, y propiciar el enlace de la enseñanzacon las actividades productivas o sociales

      En este apartado nos habla de la alfabetización digital pero dentro de las instituciones públicas cada vez hay menos presupuesto y no hay buenos laboratorios de computación.

    8. prohíbe taxativamente a los representantes legales de los es-tudiantes, así como a los docentes y a los directivos de los establecimientos educativos“promover o provocar la paralización del servicio educativo”. En la disposición generalprimera, la Ley también establece que, “considerando que la educación es un derechohumano a la vez que un servicio público fundamental, se prohíbe a todos los miembrosde la comunidad educativa, promover o provocar deliberadamente la paralización delservicio educativo. Ninguna causa o circunstancia, excepto la que derive del caso for-tuito o de fuerza mayor, justificará la interrupción de las actividades educativas

      muchas de las veces padres de familia hacen plantones con el objetivo de dar una queja de un docente o de alguna inconsistencia, en este caso, creo que hay pro y contras de que se haga estas paralizaciones, bueno porque socializan su malestar para dar una solución y malo porque afecta a toda la comunidad educativa, y es el mismo caso de los docentes o dirtectivos.

    9. La formación inicial de docentes y otros profesionales educativos en el Ecuador hatenido dificultades, y esa puede ser una de las causas de las carencias del SistemaEducativo Nacional. La Constitución de la República procura resolver este problema y,en su disposición transitoria vigésima, establece que el Gobierno Nacional creará unainstitución educativa superior, dirigida por el Ministerio de Educación, “con el objetivode fomentar el ejercicio de la docencia y de cargos directivos, administrativos y de apo-yo en el sistema nacional de educación”

      Es fundamental que el país tenga una universidad o varias con el fin de crear nuevos docentes, ya que desde las diferentes profesiones si se puede ejercer la docencia pero si falta pedagogía.

    10. Los estudiantes que cometan actos de deshonestidad académica serán sometidos alas acciones disciplinarias establecidas en el presente Reglamento y además recibi-rán una calificación de cero en la tarea o el examen en que haya cometido el acto dedeshonestidad académica.

      Los actos de deshonestidad académica son sometidos a las acciones disciplinarias. Resulta alarmante como los estudiantes copian cualquier información que encuentran en internet sin siquiera leer.

    11. Tipos de evaluación. La evaluación estudiantil puede ser de los siguientestipos, según su propósito:1. Diagnóstica: Se aplica al inicio de un período académico (grado, curso, qui-mestre o unidad de trabajo) para determinar las condiciones previas con que elestudiante ingresa al proceso de aprendizaje

      La evaluación estudiantil puede ser diagnóstica, al inicio del período académico; formativa, durante el proceso de aprendizaje; y sumativa, al final del curso o trimestre. Por lo tanto, la evaluación se realiza a lo largo del año lectivo.

    12. El docente tutor de grado o curso es el principal interlocutor entre la institución y los re-presentantes legales de los estudiantes. Está encargado de realizar el proceso de evalua-ción del comportamiento de los estudiantes a su cargo, para lo cual debe mantener unabuena comunicación con todos los docentes del grado o curso.

      Ser docente tutor es muy demandante porque hay que estar pendiente del curso designado, coordinar todas las actividades, comunicar a los representantes, dirigir reuniones y juntas de curso, preguntar a todos los docentes por el rendimiento académico y comportamiento de los estudiantes a cargo...

    13. Recibir educación escolarizada o no escolarizada, formal o informal a lo largo desu vida que, complemente sus capacidades y habilidades para ejercer la ciuda-danía y el derecho al Buen Vivir

      Este literal me parece muy importante por que las personas no tenemos un limite de edad para comenzar o continuar con nuestros estudios, en muchos de los casos el recurso económico no permite que se avance con los estudios pero no significa que las personas no tengamos la necesidad de aprender o seguirnos preparando

    14. Una educación que desarrolle sus potencialidades y habilidades para su integracióny participación en igualdad de condiciones. Se garantizará su educación dentro dela educación regular.

      Considero que dentro de este apartado se busca el bien común para los ESTUDIANTES sin importar si tienen capacidades especiales o no, considero que todos tienen el derecho de pertenecer a la institución educativa de su agrado y desarrollar sus habilidades con la ayuda de maestros capacitados.

    15. De estos principios constitucionales se deriva el artículo 47de la LOEI, así como los artículos 227, 228, 229 y 230 del Reglamento, los cualesestablecen que el Ministerio de Educación, a través de su planta central y de susniveles desconcentrados, promoverá el acceso y permanencia en el sistema edu-cativo de las personas con necesidades educativas especiales, asociadas o no a ladiscapacidad. Este mandato se cumple ya sea mediante la asistencia a clases enun establecimiento educativo especializado o mediante su inclusión en un estable-cimiento de educación escolarizada ordinaria

      Es correcto darle importancia a este apartado ya que dentro de muchas familias podemos tener un familiar que tenga la necesidad de aprender pero con un trato especial, y sobre todo no excluir a las personas con capacidades especiales de los establecimientos de educación ordinario, es claro que existen centros educativos especializados, pero mientras exista la debida capacitación y preparación de los maestros dentro de instituciones educativas las personas en condiciones vulnerables serán tomadas en cuenta no por sus capacidades especiales si no como un estudiante ordinario.

    16. Se apunta a la excelencia en los docentes con un escalafón auténticamentemeritocrático que asegura una remuneración justa y digna.Bajo el marco legal anterior, los docentes fiscales tenían los sueldos más bajos de to-dos los servidores públicos, aportaban a la seguridad social sobre una fracción de suingreso, y su carrera, que no daba alternativas profesionales, se regía por un escalafónexcesivamente complicado que no enfatizaba el mérito académico sino la antigüedad.El nuevo marco legal cambia completamente esta situación, con los siguientes logrosprincipales:• Mejora sustancialmente los sueldos docentes, pues la LOEI determina un incre-mento notable del salario de los maestros, que en algunos casos supera el cien porciento;• Consigna una aportación justa a la seguridad social, sobre la totalidad de su ingreso;• Permite a los docentes optar por diferentes rutas profesionales alternativas, talescomo la de director o rector de establecimientos educativos, la de asesor educativo,la de auditor educativo y la de docente-mentor, y• Establece un escalafón simplificado que ya no privilegia la antigüedad, sino facto-res tales como la formación académica de los docentes, sus estudios de actua-lización, su experiencia y sobre todo su desempeño profesional (demostrado enevaluaciones y en otras evidencias), y establece distinciones y ascensos correla-cionados a sus propios méritos. Así, el artículo 349 de la Constitución institucio-naliza un sistema de evaluación del desempeño docente y lo vincula a la políticasalarial en todos los niveles.Así, el nuevo marco legal estipula la existencia de un sistema de estímulos dirigido a darreconocimiento a los mejores educadores, y dispone que la mejora de los ingresos decada docente sea consecuencia directa de su buen desempeño en el proceso educa-tivo que tenga a su cargo.19. Se garantiza la selección de los mejores docentes con concursos de méritosy oposición rigurosos y transparentes.Anteriormente, los docentes que ingresaban al magisterio no siempre cumplían conlos requisitos básicos necesarios, en parte porque el marco legal no los especifi-

      Desde este punto de vista el articulo busca mejorar la ley de escalafón docente el cambio parece valedero, pero debido de acompañarse por políticas educativas que habrán los periodos de ascenso y recategorización cada año por ahora los docentes nos encontramos estancados en una categoría a pesar de cumplir con los requisitos establecidos

    17. Este servicio público que es la educación puede ser ofrecido a través de institucionespúblicas, fiscomisionales y particulares (Art. 345 de la Constitución), con lo cual se ga-rantiza la libertad de enseñanza (determinada también en el Art. 29 de la Constitución), yse consagra la existencia de la educación particular (confesional o laica), así como de laeducación fiscomisional, siempre que cumplan con ciertas condiciones que respondenal carácter público del servicio educativo, entre las que se destaca en el mismo artículo345 el que en todos los centros educativos se deben ofrecer “sin costo servicios decarácter social y de apoyo psicológico, en el marco del sistema de inclusión y equi-

      Este articulo busca normar los servicios educativos que se prestan en instituciones publicas y fiscales para que la educación bajo ningún concepto sea vista como algo lucrativo, que perjudique a todo aquel que no tenga el recurso de costearla asegurando de esta manera el derecho a la gratuidad de la educación.

    18. prohíbe taxativamente a los representantes legales de los es-tudiantes, así como a los docentes y a los directivos de los establecimientos educativos“promover o provocar la paralización del servicio educativo”. En la disposición generalprimera, la Ley también establece que, “considerando que la educación es un derechohumano a la vez que un servicio público fundamental, se prohíbe a todos los miembrosde la comunidad educativa, promover o provocar deliberadamente la paralización delservicio educativo. Ninguna causa o circunstancia, excepto la que derive del caso for-tuito o de fuerza mayor, justificará la interrupción de las actividades educativas”. De estamanera, los paros de actividades con las consiguientes pérdida de clases, empobreci-miento de la calidad de la educación pública y violación del derecho a la educación deniñas, niños y adolescentes que aquellos ocasionaban son cosa del pasado.

      Este numeral me parece que es el más interesante por analizar dentro del marco que se generó durante la pandemia del 2020, que acciones tomó el estado para garantizar el acceso a la educación a estudiantes de escasos recursos econmómicos sin acceso a internet.

    1. |

      La barra vertical | se utiliza en Pharo para representar el operador lógico OR (o). Asimismo, se utiliza para combinar dos expresiones booleanas.

    1. BinarySearchTree

      二叉搜索树(Binary Search Tree,简称BST)是一种特殊的二叉树,它满足下列性质:

      每个节点包含一个键(key)和关联的值。
      每个节点的键都大于其**左子树中任意节点**的键。
      每个节点的键都小于其**右子树中任意节点**的键。
      左右子树也都是二叉搜索树。
      

      因此,在二叉搜索树中,所有的元素都是以某种顺序排列的,这使得查找、插入和删除操作可以在平均和最坏情况下具有对数时间复杂度,即时间复杂度为O(log n),其中n是树中元素的数量。这种性质使得二叉搜索树成为数据结构中非常有效的搜索和排序工具。

    1. |

      La barra vertical | se utiliza en Pharo para representar el operador lógico OR (o). Asimismo, se utiliza para combinar dos expresiones booleanas.

    Annotators

    1. Las definiciones anteriores no definen con precisión lo que es un evento.

      Es mejor quitar la línea. O se puede dejar pero escribirle algo más, podría ser: Las definiciones....lo que es un evento, ya que aunque un evento siempre será...muestral, en espacios muestrales...

    1. digital learning increased in market demand over the last decade

      Parece-me que esta é a maior questão. O desejo de uma transição para o digital de modo a facilitar o ensino e aumentar o mercado. Imagino que um destes dias possamos tirar um curso superior totalmente online, até talvez mesmo sem qualquer intervenção humana, sem professor, sem contactos, só IA... Não sei se será o mesmo!

    2. This research has had the potential to shed some light, become a pathfinder even, on not only the complexities of designing online courses that meet the complex criteria of the CoI framework, but also simply to highlight the merit and importance in utilising a structured, well-rehearsed and appropriate pedagogy approach to any design of an online course. While one would think this advice stands to reason, the truth is that the current experience of the average online student with their teacher is one of great disappointment [43,44]

      Em verdade a experiência do aluno online pode ser decepcionante se a abordagem pedagógica não for estruturada ou apropriada. Assim é importante definir claramente os objetivos de aprendizagem e conhecer muito bem o publico alvo. Neste contexto a escolha de tecnologias adequadas será mais assertiva e permitirá promover a interatividade e estimular a colaboração entre os alunos, mudando a sua visão da experiencia de aprendizagem online.

    3. 1º artigo com 10 anos, o que para uma investigação científica seria em "exagero", mas tão actual em conteúdo e reflexões; 2º é impossível depois de ler o artigo e os comentários e não comparar o VideoAnt com o Hypothes.is; 3º este Hypothes.is é como uma anotação colaborativa que nos permite (formadores e formandos) destacar, comentar e discutir os conteúdos em causa, mas senti-o muito menos intuitivo, menos digital-friendly quando comparado com o VideoAnt; 4º apesar desta nota negativa parece-me por outro lado que o Hypothes.is é mais abrangente, pois permite notas/textos/comentários em páginas da web em geral e não só de artigos, e segundo me parece tem a possibilidade dos nossos comentários serem mesmo em forma de vídeo o que acho que o torna uma mais valia! Celso Teixeira

    1. Oh shame and pain: O woe is me! Would I could die in my misery!

      This conversation is between the attendant and nurse, but it is conveyed internally within the Nurse's mind. The conversation is pertaining to the affair pertaining to Medea, Jason, and Glause. The attendant is shown to have a much harsher tone overall compared to the Nurse, while they are seen to be more optimistic for the future to come and the outcome for everyone. This quote pertains to the Nurse's internal dialogue and is portraying her much more hopeless inner thoughts. She seems to be putting up a much more positive front on the outside to protect Medea, but she is a worried mess on the inside.

    1. Vlasov etal. [2] introduced the Recurrent Embedding Dialogue Pol-icy (REDP) architecture. The ablation study in this workhighlighted that the improved performance of REDP isdue to an attention mechanism over the dialogue historyand a copy mechanism to recover from unexpected userinput. This modification to the standard RNN structureenables the dialogue policy to ‘skip’ specific turns in thedialogue history and produce an encoder state which isidentical before and after the unexpected input.

      Vlasov và cộng sự đã phát triển kiến trúc REDP. Thực nghiệm cho thấy REDP có cải thiện nhờ vào cơ chế chú ý trên lịch sử hội thoại và cơ chế sao chép để khôi phục từ đầu vào không mong muốn của người dùng. 2 cải tiến này so với kiến trúc RNN tiêu chuẩn cho phép DP có thể bỏ qua các lượt cụ thể trong lịch sử hội thoại và đưa ra được các trạng thái encoder tương tư nhau ở trước và sau đầu vào không mong muốn

    1. don

      ¿Es un ejemplo, cierto? Causaría menos confusión si escribes Ejemplo 1.1 ... o si lo ligas a la línea anterior comentando que es un ejemplo.

    1. Résumé de la vidéo [00:00:01][^1^][1] - [00:24:06][^2^][2]:

      La première partie de la vidéo explore l'histoire de la psychanalyse et son développement par Sigmund Freud. Elle examine les origines de concepts tels que l'inconscient et la neurologie, et comment Freud a été influencé par des figures telles que Charcot et Janet.

      Points forts: + [00:00:17][^3^][3] Origines de la psychanalyse * Remonte à l'Antiquité * Freud et l'inconscient + [00:01:19][^4^][4] Neurologie et psychologie * Lien entre cerveau et esprit * Influence de Charcot et Janet + [00:03:08][^5^][5] Freud à la charnière * Transition vers la psychiatrie * Études de neurologie + [00:10:12][^6^][6] Influence de l'hypnose * Charcot et l'hystérie * Janet et la psychologie clinique + [00:17:02][^7^][7] De l'hypnose à la psychanalyse * Limites de l'hypnose * Naissance de la psychanalyse + [00:20:59][^8^][8] Cas fondateur de Freud * Étude de cas d'Anna O. * Thérapie cathartique Résumé de la vidéo 00:24:08 - 00:49:04: La partie 2 de la vidéo aborde la psychanalyse, en se concentrant sur l'histoire d'Anna O., les théories de Freud sur le refoulement et la séduction, et l'évolution de ses idées sur la sexualité et le développement psychique.

      Points forts: + [00:24:08][^1^][1] Anna O. et la psychanalyse * Cas fondateur de la psychanalyse * Cure par la parole + [00:26:01][^2^][2] Théories de Freud * Introduction du refoulement * Théorie de la séduction + [00:28:30][^3^][3] Évolution des idées de Freud * Abandon de la théorie de la séduction * Naissance de la théorie du fantasme + [00:33:06][^4^][4] Vision de Freud sur les femmes * Infériorité et envie du pénis * Impact sur la justice et la moralité + [00:37:02][^5^][5] Stades de développement selon Freud * Oral, anal, phallique, latence, génital * Fixations et traits de caractère + [00:43:35][^6^][6] Le transfert en psychanalyse * Relation patient-analyste * Importance dans la thérapie Résumé de la vidéo [00:49:08][^1^][1] - [00:59:03][^2^][2]:

      La partie 3 de la vidéo discute de la psychanalyse, en particulier les idées de Freud sur l'inconscient, les pulsions et la pulsion de mort. Jacques Van Rillaer examine les critiques de la psychanalyse et l'impact historique de Freud.

      Points forts: + [00:49:08][^3^][3] Freud et l'inconscient * L'inconscient contient des souvenirs et pulsions problématiques + [00:50:06][^4^][4] Créativité vs pulsions * Freud ne voyait pas l'inconscient comme une source de créativité + [00:51:35][^5^][5] Introduction de la pulsion de mort * Freud remplace la dualité des pulsions par la vie et la mort + [00:52:27][^6^][6] La pulsion de mort explique * La répétition d'expériences malheureuses et l'agressivité + [00:53:18][^7^][7] Le succès de Freud * Manque de thérapies alternatives et simplicité de ses théories + [00:56:33][^8^][8] Freud comme révolutionnaire * Se compare à Copernic et Darwin dans l'impact sur la pensée humaine

    1. Capítulo 9. O concurso “A Aldeia Mais Portuguesa de Portugal” (1938)

      Olá! Bem-vindos(as)! Convido-vos a ler e discutir o texto da autoria do antropólogo Pedro Félix sobre o Concurso da Aldeia Mais Portuguesa de Portugal.

      Começo por lançar uma questão para debate: Qual a relação desta iniciativa com o processo de folclorização?

      Bom trabalho!

    1. Es un objetivo de la Autoridad Educativa Nacional di-señar y asegurar la aplicación obligatoria de un currí-culo nacional, tanto en las instituciones públicas, mu-nicipales, privadas y fiscomisionales, en sus diversosniveles: inicial, básico y bachillerato, y modalidades:presencial, semipresencial y a distancia. [...] El Currí-culo podrá ser complementado de acuerdo con lasespecificidades culturales y peculiaridades propias dela región, provincia, cantón o comunidad de las diver-sas Instituciones Educativas que son parte del SistemaNacional de Educación.

      Con este articulo se norma que instituciones publicas y privadas utilicen el mismo currículo de manera obligatoria, para que no exista la idea que porque una institución es particular va trabajar de forma apartada a las directrices del Ministerio de Educación .

    2. En el año 2021, el Ministerio de Educaciónexpide elCurrículo priorizado con énfasisen competencias comunicacionales,matemáticas, digitales y socioemocionales,el cual está separado por subniveles yes aplicable en la modalidad presencial,semipresencial o a distancia, con el fin defortalecer estas competencias.

      Este nuevo currículo surge como una respuesta a muchas necesidades educativas que se evidenciaron después de pasar la pandemia por Covid 19 donde se hace énfasis en las competencias para fortalecerlas.

    3. Cuando los estudiantes escuchan oleen un texto y lo comprenden o cuan-do producen un texto oral o escrito yel destinatario es capaz de compren-derlo, se trata de un proceso de desa-rrollo de las competencias comunica-cionales

      Es indispensable saber como enseñar a los estudiantes las estrategias para leer un texto y así se aprende a entender las diferentes culturas, y tradiciones.

    4. Lasmetodologías activas permiten colocaral estudiante en el centro de los apren-dizajes, motivan además la curiosidad,la investigación, la generosidad intelec-tual y mejoran la comunicación entre losmiembros de la comunidad educativa.

      Es importante que los métodos que vamos a utilizar con nuestros estudiantes no sean pasivos por el contrario deben ser métodos en los cuales nuestros estudiantes interactúen, motivándolos a despertar su curiosidad y por ende su interés a la lectura o investigación para que a través de esto ellos puedan desarrollar un pensamiento critico y mejorar la comunicación dentro y fuera de su salón de clases.

    1. The only issue left to tackle is the performance issue. In many cases it actually turns out to be a non-issue because of the clustered index on AgreementStatus (AgreementId, EffectiveDate) - there's very little I/O seeking going on there. But if it is ever an issue, there are ways to solve that, using triggers, indexed/materialized views, application-level events, etc.
    1. ‘Master,’ I said, ‘tell thou, ere making pause, Who Fortune is of whom thou speak’st askance, Who holds all worldly riches in her claws.’ ‘O foolish creatures, lost in ignorance!’ He answer made.

      Here is another example of Dante implementing his own ideas of morality and virtuous acts into his comedy, explaining how Dante views those who seek only worldly riches as opposed to knowledge, believing these people to be foolish in the eyes of God. This reflects heavily on Dante, being born into a rich family, and is demonstrative of his ideas of wealth, as he was able to work in politics, literature, and a multitude of other topics that someone of a lower-class background would likely not be able to involve themselves with because of their own wealth insecurity and need to work to provide. In this way, it reflects an irony onto Dante, as he, being born into a family of wealth, has less of an understanding of a need to work, and could, instead, work in many different places and topics, bouncing around each of them.

      SANTAGATA, MARCO, and Richard Dixon. Dante: The Story of His Life. Harvard University Press, 2016. JSTOR, https://doi.org/10.2307/j.ctvjsf5bx. Accessed 7 Mar. 2024.

    Annotators

    1. Galata kulesi önünde kanlı gelinlikle evlilik teklifi

      Diğer destek değil de Protesto mu desek tür olarak, sanki o şekilde daha iyi kategorize olacak. Tüm protesto örneklerini göster deyince

    1. Author Response

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

      Reviewer #1 (Recommendations for the Authors):

      (1) Within the section on "optimized antigen retrieval", the authors mentioned that weak immunolabelling and strong non-specific labelling may be due to inadequate antigen retrieval. I wonder whether this interpretation is accurate. Could it also be due to inadequate antibody penetration?

      We appreciate the reviewer's comment and have revised our text to improve clarity. Regarding the SDS-electrophoresed sample (Figure S1a right), we acknowledge that the brain-surrounding background noise indicates insufficient antibody penetration. However, in the FLASH-processed sample (Figure S1a left), the background signal is uniformly distributed throughout the entire brain. Therefore, we conclude that incomplete antibody penetration is unlikely under this condition. Below is the revised paragraph:

      Revised manuscript, line 62-66: “We observed that both FLASH-processed and SDS-electrophoresed samples showed weak tyrosine hydroxylase (TH, a marker of dopaminergic neurons) signal (Figure S1a, Supporting Information). Additionally, we noticed that the FLASH-processed samples had almost no signal of NeuN, a marker of neuronal nuclei (Figure S1b left, Supporting Information), and exhibited strong non-specific background noise (Figure S1a left, Supporting Information). The presence of this background noise is considered an indicator of inadequate antigen retrieval.[48]”

      • Also, the authors mentioned the use of FLASH protocol and SDS-based electrophoresis for delipidation which were not described in the methods section.

      We have included the information in the revised Materials and Methods.

      Revised manuscript, line 418-426: S”HIELD processing, SDS-electrophoretic delipidation and FLASH delipidation. PFA-fixed specimens were incubated in SHIELD-OFF solution at 4 °C for 96 hours, followed by incubation for 24 hours in SHIELD-ON solution at 37 °C. All reagents were prepared using SHIELD kits (LifeCanvas Technologies, Seoul, South Korea) according to the manufacturer's instructions. For SDS-electrophoretic delipidation, SHIELD-processed specimens were placed in a stochastic electro-transport machine (SmartClear Pro II, LifeCanvas Technologies, Seoul, South Korea) running at a constant current of 1.2 A for 5-7 days. For FLASH delipidation, the SHIELD-processed specimens were placed in FLASH reagent (4% w/v SDS, 200 mM borate) and then incubated at 54 ℃ for 18 hours.[47] The delipidated specimens were washed with PBST at room temperature for at least 1 day.”

      • In addition, tyrosine hydroxylase (TH) should be a marker of "monoaminergic" neurons rather than specifically "dopaminergic" neurons.

      We appreciate the reviewer's correction. It is true that tyrosine hydroxylase (TH) is a marker for neurons that contain dopamine, norepinephrine, and epinephrine (catecholamines). However, the adrenergic and noradrenergic neurons are relatively few and are mostly located in the medulla and brain stem. Since we only monitoring the brain in this study, we wish to keep TH as an indicator of dopaminergic neurons.

      (2) It was mentioned that tissue integrity was retained following heating treatment during the MOCAT protocol. It would be useful to demonstrate any differences in structural distortion, if any, with before and after images with different delipidation agents.

      We have provided an additional supplementary figure (Figure S5 in the revised manuscript) to display the mouse brain at different stages of the MOCAT protocol, including pre-delipidation, post-delipidation, and post-RI-matching, to demonstrate the tissue integrity.

      Revised manuscript, line 135-137: “Figure S5 shows the gross views of the same mouse brain after undergoing 4% PFA fixation, paraffin processing, optimized antigen retrieval, and RI-matching, demonstrating intactness of the brain shape and preservation of tissue integrity.”

      (3) In this study, the authors have demonstrated the protocol could be successfully applied to FFPE specimens up to 15 years old. However, archival brain bank materials often have brain tissues with extended formalin fixation time. It may be useful to demonstrate that this technique can be utilised on FFPE tissues with long formalin fixation times.

      We appreciate the reviewer's suggestions. We have included an additional supplementary figure (Figure S6) to demonstrate the application of MOCAT to 3-month fixed mouse brain hemispheres. Although the long-term fixed specimens exhibited reduced TH intensity and S/N ratio, the major dopaminergic regions were labeled, and magnified images revealed details of cell bodies and neuronal fibers. These results suggest that MOCAT has the potential to be applied to long-term fixed specimens.

      The fluorescence intensity was more affected by fixation with formalin, which is methanol-stabilized and stronger, than with PFA. This indicates that a stronger antigen retrieval method may be a possible solution. However, achieving the right balance between antigen retrieval efficiency and tissue integrity will require additional testing and investigation.

      Revised manuscript, line 163 to 167: “We also applied MOCAT to 3-month fixed mouse brain hemispheres (Figure S6). Although the long-term fixed specimens exhibited reduced TH intensity and S/N ratio, the major dopaminergic regions were labeled, and magnified images revealed clear details of cell bodies and neuronal fibers. These results suggest that MOCAT has the potential to be applied to long-term fixed specimens.”

      Revised manuscript, line 346-351: “In the demonstration of MOCAT to 3-month fixed specimens, we observed that pontine reticular nucleus (Figure S6A, yellow arrowheads) lose TH-positive signals after long-term fixation. The fluorescence intensity was more affected by fixation with formalin, which is methanol-stabilized and stronger, than with PFA. The results indicate that a stronger antigen retrieval method may be a possible solution. However, achieving the right balance between antigen retrieval efficiency and tissue integrity will require additional testing and investigation.”

      (4) Whilst it is encouraging to see this protocol enables multi-round immunolabelling, further work is required to demonstrate there is no cross-reactivity in subsequent rounds of immunostaining following bleaching (e.g. Non-specific secondary antibody binding).

      We appreciate the reviewer for noting their concern and providing suggestions. To address this issue, we have examined the results of the second to fourth rounds of multi-round staining, as shown in Figure 3. In all three sequential rounds, we utilized rabbit primary antibodies and the same secondary antibodies. Our observations under a 3.6x objective (NA = 0.2) did not reveal any colocalization with the staining from the previous round. Hence, we conclude that cross-reactivity is not significant. However, we acknowledge the need for more comprehensive testing to completely rule out the possibility of cross-reactivity, such as employing antibodies from different hosts or utilizing different types of secondary antibodies (e.g., IgG, Fab2).

      Revised manuscript line 189-191: “The brain shape and structural integrity remained after 4 rounds of immunolabeling, and there is no cross-reactivity in subsequent rounds of immunostaining following bleaching. (Figure S11).”

      • Also, how was the structural integrity maintained for tissues after multiple rounds of heat-induced epitope retrieval?

      We have provided an additional supplementary figure (Figure S11 in the revised manuscript) to demonstrate the structural integrity after 4 rounds of immunolabeling.

      Revised manuscript line 189-191: “The brain shape and structural integrity remained after 4 rounds of immunolabeling, and there is no cross-reactivity in subsequent rounds of immunostaining following bleaching (Figure S11).”

      (5) It may be useful to have a side-by-side comparison in staining quality with equivalent sizes of rodent and human brain tissues as there appeared to be a reduction in clarity and staining quality at greater imaging depth for human tissues.

      We have provided an additional supplementary figure (Figure S12) to show the fluorescent images of TH- and Lectin-labeling in 1mm-thick human and mouse brain tissues at depths of 100 um, 500 um, and 900 um. For millimeter-sized samples, both human and mouse brains showed comparable levels of transparency, with no noticeable reduction in fluorescence signal at varying depths. In our forthcoming studies, we plan to conduct a more comprehensive comparison of centimeter-sized human and mouse brain tissues.

      (6) Lectin staining is used throughout this study to label vasculature of the brain. How specific is this as compared with other vasculature markers such as CD31?

      We appreciate the reviewer for addressing their concern. Lectins are nonimmune-origin carbohydrate-binding proteins that have been utilized to label the surface of the blood vessel lumen. On the other hand, CD31, CD34, etc. are immunomarkers of vascular endothelial cells. Numerous references have confirmed that lectin staining consistently co-localizes with CD31 immunoreactivity (Battistella et al. 2021; Miyawaki et al. 2020). However, in tumors, blood vessels lacking a lumen may display CD31 positive/Lectin negative conditions (Morikawa et al. 2002).

      (7) When discussing the applicability of MOCAT on the astrocytoma mouse model, there is a bit of confusion with regard to the terminology. As astrocytoma by default will be comprised of astrocytes, it may be useful to describe the tumour astrocytes as ASTS1CI-GFP positive astrocytes and immunolabelled astrocytes as GFAP-positive astrocytes.

      We thank the reviewer for their suggestions. To avoid confusion for readers, we have made modifications to the content and labeling of Figure 6A.

      Revised manuscript, line 213-219: “…we subjected an intact FFPE brain from an astrocytoma mouse model (see Materials and Methods) to the MOCAT pipeline to label tumor cells (ASTS1CI-GFP positive astrocytes) and GFAP-positive astrocytes (Figure 6A, C). Accordingly, we could segment GFAP-positive astrocytes surrounding the tumor (Figure 6B, D, and E) and classify them according to their distances from the tumor cells. Statistical analysis (Figure 6F) revealed that nearly half of the GFAP-positive astrocytes were within the tumor, with 63.9% being located near the tumor surface (±200 μm).”

      (8) Within the methods section, further details of the antibodies such as the clonality and immunogen should be included in the supplementary table.

      We appreciate the reviewer for their suggestions. In the revised version, we have included these details in Supplementary Table 1.

      • Furthermore, there is inadequate detail regarding multi-round immunolabelling and the precise timing of immunolabelling including lectin staining, various imaging parameters including the working distance of the lens and excitation laser used.

      We have added the experimental details of multi-round staining for Figure 3 in Supplementary Table 3. This table now includes information about the amounts and types of chemicals and antibodies used, as well as the laser wavelengths used for each round. The staining conditions (including labeling time, temperature, and buffer used) have been disclosed in Materials and Methods (see MOCAT pipeline/Electrophoretic immunolabeling). Furthermore, we have included the working distance and NA value of the objective lens used in MOCAT pipeline/Volumetric imaging and 3D visualization subsection.

      Revised manuscript, line 464-479: “Electrophoretic immunolabeling (active staining). The procedure was modified from the previously published eFLASH protocol[15] and was conducted in a SmartLabel System (LifeCanvas Technologies, Seoul, South Korea). The specimens were preincubated overnight at room temperature in sample buffer (240 mM Tris, 160 mM CAPS, 20% w/v D-sorbitol, 0.9% w/v sodium deoxycholate). Each preincubated specimen was placed in a sample cup (provided by the manufacturer with the SmartLabel System) containing primary, corresponding secondary antibodies and lectin diluted in 8 mL of sample buffer. Information on antibodies, lectin and their optimized quantities is detailed in Supplementary Table 1. The specimens in the sample cup and 500 mL of labeling buffer (240 mM Tris, 160 mM CAPS, 20% w/v D-sorbitol, 0.2% w/v sodium deoxycholate) were loaded into the SmartLabel System. The device was operated at a constant voltage of 90 V with a current limit of 400 mA. After 18 hours of electrophoresis, 300 mL of booster solution (20% w/v D-sorbitol, 60 mM boric acid) was added, and electrophoresis continued for 4 hours. During the labeling, the temperature inside the device was kept at 25 ℃. Labeled specimens were washed twice (3 hours per wash) with PTwH (1× PBS with 0.2% w/v Tween-20 and 10 μg/mL heparin),[23] and then post-fixed with 4% PFA at room temperature for 1 day. Post-fixed specimens were washed twice (3 hours per wash) with PBST to remove any residual PFA.”

      Revised manuscript, line 483-490: “Volumetric imaging and 3D visualization. For centimeter-scale specimens, images were acquired using a light-sheet microscope (SmartSPIM, LifeCanvas Technologies, Seoul, South Korea) with a 3.6x customized immersion objective (NA = 0.2, working distance = 1.2 cm). For samples <3 mm thick, imaging was performed using a multipoint confocal microscope (Andor Dragonfly 200, Oxford Instruments, UK) with objectives that were UMPLFLN10XW (10x, NA = 0.3, working distance = 3.5 mm), UMPLFLN20XW (20x, NA = 0.5, working distance = 3.5 mm), UMPLFLN40XW (40x, NA = 0.8, working distance = 3.3 mm). 3D visualization was performed using Imaris software (Imaris 9.5.0, Bitplane, Belfast, UK).”

      • Also, since refractive index homogenisation is an important step in tissue-clearing experiments, it may be useful to describe the components of NFC1 and NFC2 solutions used and provide images of the "cleared" tissues.

      We have included the image of a cleared mouse brain in Figure S5. Additionally, we have provided the refraction index of NFC1 and NFC2 in Materials and Methods (see MOCAT pipeline/Refractive index matching). However, the composition of NFC1 and NFC2, being commercialized products from Nebulem (Taiwan), is non-disclosable.

      Reviewer #2 (Public Review):

      Major Weaknesses:

      • There is no evidence of actual transparency of the entire mouse brain across different treatments. The suggested protocol is very good at removing lipids (as assessed by DiD staining) and by results of fluorescence registration deep within the brain. BUT, since in many places of the manuscript authors speak of "transparency" the reader will expect the typical picture in which control and processed brains are on top of a white graphical pattern that would evidence transparency (see as an example Figure 1 and 2 of Wan et al. 2018 (Neurophotonics. 2018 Jul;5(3):035007. doi: 10.1117/1.NPh.5.3.035007.)

      We thank the reviewer for their suggestions. We have provided an additional supplementary figure (Figure S5 in the revised manuscript) to demonstrate the transparency.

      • The manuscript lacks clarity on the applicability of MOCAT to regular formalin-fixed tissue and tissues other than the brain.

      We appreciate the reviewer's suggestions. We have included an additional supplementary figure (Figure S6) to demonstrate the application of MOCAT to a 3-month regular formalin-fixed mouse brain hemisphere. We observed that the major dopaminergic regions were still labeled, although with reduced intensity and S/N ratio. We also observed that the fluorescence intensity was more affected in formalin, which is methanol-stabilized and stronger, than in PFA, implying that a stronger antigen retrieval method may be possible to rescue the intensity. However, achieving the right balance between antigen retrieval efficiency and tissue integrity will require additional testing and investigation.

      Revised manuscript, line 163 to 167: “We also applied MOCAT to 3-month fixed mouse brain hemispheres (Figure S6). Although the long-term fixed specimens exhibited reduced TH intensity and S/N ratio, the major dopaminergic regions were labeled, and magnified images revealed clear details of cell bodies and neuronal fibers. These results suggest that MOCAT has the potential to be applied to long-term fixed specimens.”

      Revised manuscript, line 346-351: “In the demonstration of MOCAT to 3-month fixed specimens, we observed that pontine reticular nucleus (Figure S6A, yellow arrowheads) lose TH-positive signals after long-term fixation. The fluorescence intensity was more affected by fixation with formalin, which is methanol-stabilized and stronger, than with PFA. The results indicate that a stronger antigen retrieval method may be a possible solution. However, achieving the right balance between antigen retrieval efficiency and tissue integrity will require additional testing and investigation.”

      Regular formalin

      We agree with the reviewer and plan to investigate the potential use of MOCAT in tissues other than the brain in our subsequent studies.

      • Insufficient information is provided on the "epoxy treatment" or "hydrogel," and a more detailed explanation is warranted.

      We appreciate the reviewer's question. In response, we have included a paragraph in the Discussion section to clarify the appropriate timing for using epoxy or hydrogel in the MOCAT pipeline. However, the harsh conditions, such as pressure and heat, caused by external forces might damage specimens. To protect specimens from the harsh conditions caused by active staining, specimens could be strengthened by treatment with epoxy or acrylamide monomer to form a tissue-epoxy or tissue-hydrogel hybrid.[29,31] Laboratories that do not have adequate devices or handle small specimens could use passive immunolabeling instead and skip the step of epoxy or hydrogel pretreatment.

      Epoxy and acrylamide hydrogel can both strengthen tissue structures. However, in this study, we only used epoxy for treatment in combination with active electrophoretic staining. To avoid confusion and improve clarity, we have made modifications to Figure 1B and included epoxy processing in the MOCAT pipeline subsection within Materials and Methods.

      Revised manuscript, line 329-340: “In Figure 1B, we propose two staining strategies for samples with thicknesses less than 500 um and greater than 1 mm: passive immunolabeling and active immunolabeling. In passive immunolabeling, antibodies penetrate and reach their targets solely through diffusion, without any additional force. It takes approximately two months to passively stain a whole mouse brain.[26,28] Compared to passive immunolabeling, active immunolabeling uses an external force, such as pressure, electrophoresis, etc., to facilitate antibody penetration and therefore significantly speed up the staining process, reducing the required staining time for a whole mouse brain to one day. However, the harsh conditions, such as pressure and heat, caused by external forces might damage specimens. To protect specimens from the harsh conditions caused by active staining, specimens could be strengthened by treatment with epoxy or acrylamide monomer to form a tissue-epoxy or tissue-hydrogel hybrid.[29,31] Laboratories that do not have adequate devices or handle small specimens could use passive immunolabeling instead and skip the step of epoxy or hydrogel pretreatment.”

      • The differences between passive and active immunolabeling, as well as photobleaching data, should be addressed for a comprehensive understanding.

      We appreciate the reviewer's question. We have included a paragraph in the Discussion section to explain the differences between passive and active immunolabeling:

      Revised manuscript, line 329-340: “In Figure 1B, we propose two staining strategies for samples with thicknesses less than 500 um and greater than 1 mm: passive immunolabeling and active immunolabeling. In passive immunolabeling, antibodies penetrate and reach their targets solely through diffusion, without any additional force. It takes approximately two months to passively stain a whole mouse brain.[26,28] Compared to passive immunolabeling, active immunolabeling uses an external force, such as pressure, electrophoresis, etc., to facilitate antibody penetration and therefore significantly speed up the staining process, reducing the required staining time for a whole mouse brain to one day.”

      Regarding the effects of photobleaching, we have added Figure S10 to demonstrate the efficiency of using our approach.

      Revised manuscript, line 184-185: After imaging, we photobleached transparent RI-matched samples using a 100W LED white light to quench the previously labeled fluorophores (Figure S10).

      • The assertion that MOCAT can be rapidly applied in hospital pathology departments seems overstated due to the limited availability of light-sheet microscopes outside research labs.

      We thank the reviewer's question. Since the imaging depth primarily relies on the working distance of the objective lens, if a long working distance objective lens (such as UMPLFLN10XW from Olympys Inc.) is available, it is also possible to scan samples up to a thickness of approximately 3.5mm. However, confocal systems require longer scanning times, and in non-optical sectioning wide-field fluorescence microscopes like the Olympus BX series or ZEISS Axio imager series, deconvolution algorithms must be utilized to eliminate out-of-focus signals.

      Additionally, the epifluorescence system may also result in reduced fluorescent intensity in the deeper regions of the sample. If the fluorescent signal of the target is weak or exceeds the working distance of the objective lens, an alternative option is to send the sample to a microscopy or imaging facility core for scanning and further analysis.

      • The compatibility of MOCAT with genetically encoded fluorescent proteins remains unclear and warrants further investigation.

      We appreciate the reviewer's question. We have included a paragraph in the Discussion section to address this limitation of MOCAT:

      Revised manuscript, line 354-361: “Fourth, MOCAT is not compatible with endogenous fluorescence due to a reduction in fluorescence intensity caused by xylene and alcohol used in paraffin processing. Researchers who need to directly observe genetically encoded fluorescent proteins can utilize tissue-clearing methods such as 3DISCO, X-CLARITY, CUBIC, etc., which have been shown to minimize the decrease in fluorescence intensity. On the other hand, if researchers need to visualize transgenic fluorescent proteins along with other biomarkers, they can use MOCAT for delipidation and boost-immunolabeling to visualize the transgenic fluorescent proteins.”

      • The control of equivalent depths in cryosections for evaluating the intensity of DiD staining should be elaborated upon.

      We have included these information in the section of Materials and Methods:

      Revised manuscript, line 428-430: “Serial 20-µm-thick cryosections were cut from mouse brain slices (2-mm thick) of various treatment conditions for subsequent DiD or Oil red O staining. For DiD staining, cryosections (that were of approximately 0-40 µm depth) were post-fixed with 4% PFA at room temperature for 5 minutes.”

      • The composition of NFC1 and NFC2 solutions for refractive index matching should be provided.

      We have provided the refraction index of NFC1 and NFC2 in Materials and Methods (see MOCAT pipeline/Refractive index matching). However, the composition of NFC1 and NFC2, being commercialized products from Nebulem (Taiwan), is non-disclosable.

      Reviewer #2 (Recommendations for the Authors):

      • A larger readership would benefit from validating imaging depths using fluorescence microscopies commonly found in pathological departments (i.e. Confocal, 2-photon, epifluorescence+deconvolution, etc).

      We thank the reviewer's recommentation. Since the imaging depth primarily relies on the working distance of the objective lens, if a long working distance objective lens (such as UMPLFLN10XW from Olympys Inc.) is available, it is also possible to scan samples up to a thickness of approximately 3.5mm. However, confocal systems require longer scanning times, and in non-optical sectioning wide-field fluorescence microscopes like the Olympus BX series or ZEISS Axio imager series, deconvolution algorithms must be utilized to eliminate out-of-focus signals.

      Additionally, the epifluorescence system may also result in reduced fluorescent intensity in the deeper regions of the sample. If the fluorescent signal of the target is weak or exceeds the working distance of the objective lens, an alternative option is to send the sample to a microscopy or imaging facility core for scanning and further analysis.

      -Investigate the compatibility of MOCAT with genetically encoded fluorescent proteins, a common target in research specimens.

      We appreciate the reviewer's question. We have included a paragraph in the Discussion section to address this limitation of MOCAT:

      Revised manuscript, line 354-361: “Fourth, MOCAT is not compatible with endogenous fluorescence due to a reduction in fluorescence intensity caused by xylene and alcohol used in paraffin processing. Researchers who need to directly observe genetically encoded fluorescent proteins can utilize tissue-clearing methods such as 3DISCO, X-CLARITY, CUBIC, etc., which have been shown to minimize the decrease in fluorescence intensity. On the other hand, if researchers need to visualize transgenic fluorescent proteins along with other biomarkers, they can use MOCAT for delipidation and boost-immunolabeling to visualize the transgenic fluorescent proteins.” References:

      Battistella, Roberta et al. 2021. “Not All Lectins Are Equally Suitable for Labeling Rodent Vasculature.” International Journal of Molecular Sciences 22(21): 22. /pmc/articles/PMC8584019/ (January23, 2024).

      Miyawaki, Takeyuki et al. 2020. “Visualization and Molecular Characterization of Whole-Brain Vascular Networks with Capillary Resolution.” Nature Communications 2020 11:1 11(1): 1–11. https://www.nature.com/articles/s41467-020-14786-z (January23, 2024).

      Morikawa, Shunichi et al. 2002. “Abnormalities in Pericytes on Blood Vessels and Endothelial Sprouts in Tumors.” The American Journal of Pathology 160(3): 985–1000.

    1. o connect the lesson to science content,Annabeth has students focus their observations on important plant parts like roots, stems, leaves,flowers; while also having her students design experiments to test ideas about plant needs, toconnect with science inquiry standards.

      Giving the purpose of the lesson and tool is imperative.

    Annotators

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    1. Author Response

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

      eLife assessment

      This study presents valuable findings characterising the genomic features of E. coli isolated from neonatal meningitis from seven countries, and documents bacterial persistence and reinfection in two case studies. The genomic analyses are solid, although the inclusion of a larger number of isolates from more diverse geographies would have strengthened the generalisability of findings. The work will be of interest to people involved in the management of neonatal meningitis patients, and those studying E. coli epidemiology, diversity, and pathogenesis.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This study uses whole genome sequencing to characterise the population structure and genetic diversity of a collection of 58 isolates of E. coli associated with neonatal meningitis (NMEC) from seven countries, including 52 isolates that the authors sequenced themselves and a further 6 publicly available genome sequences. Additionally, the study used sequencing to investigate three case studies of apparent relapse. The data show that in all three cases, the relapse was caused by the same NMEC strain as the initial infection. In two cases they also found evidence for gut persistence of the NMEC strain, which may act as a reservoir for persistence and reinfection in neonates. This finding is of clinical importance as it suggests that decolonisation of the gut could be helpful in preventing relapse of meningitis in NMEC patients.

      Strengths:

      The study presents complete genome sequences for n=18 diverse isolates, which will serve as useful references for future studies of NMEC. The genomic analyses are high quality, the population genomic analyses are comprehensive and the case study investigations are convincing.

      We agree

      Weaknesses:

      The NMEC collection described in the study includes isolates from just seven countries. The majority (n=51/58, 88%) are from high-income countries in Europe, Australia, or North America; the rest are from Cambodia (n=7, 12%). Therefore it is not clear how well the results reflect the global diversity of NMEC, nor the populations of NMEC affecting the most populous regions.

      The virulence factors section highlights several potentially interesting genes that are present at apparently high frequency in the NMEC genomes; however, without knowing their frequency in the broader E. coli population it is hard to know the significance of this.

      We acknowledged the limitations of our NMEC collection in the Discussion. We agree the prevalence of virulence factors in our collection is interesting. The limited size of our collection prevented further evaluation of the prevalence of these virulence factors in a broader E. coli population.

      Reviewer #2 (Public Review):

      Summary:

      In this work, the authors present a robust genomic dataset profiling 58 isolates of neonatal meningitis-causing E. coli (NMEC), the largest such cohort to be profiled to date. The authors provide genomic information on virulence and antibiotic resistance genomic markers, as well as serotype and capsule information. They go on to probe three cases in which infants presented with recurrent febrile infection and meningitis and provide evidence indicating that the original isolate is likely causing the second infection and that an asymptomatic reservoir exists in the gut. Accompanying these results, the authors demonstrate that gut dysbiosis coincides with the meningitis.

      Strengths:

      The genomics work is meticulously done, utilizing long-read sequencing.

      The cohort of isolates is the largest to be sampled to date.

      The findings are significant, illuminating the presence of a gut reservoir in infants with repeating infection.

      We agree

      Weaknesses:

      Although the cohort of isolates is large, there is no global representation, entirely omitting Africa and the Americas. This is acknowledged by the group in the discussion, however, it would make the study much more compelling if there was global representation.

      We agree. In the Discussion we state this is likely a reflection of the difficulty in acquiring isolates causing neonatal meningitis, in particular from countries with limited microbiology and pathology resources.

      Reviewer #3 (Public Review):

      Summary:

      In this manuscript, Schembri et al performed a molecular analysis by WGS of 52 E. coli strains identified as "causing neonatal meningitis" from several countries and isolated from 1974 to 2020. Sequence types, virulence genes content as well as antibiotic-resistant genes are depicted. In the second part, they also described three cases of relapse and analysed their respective strains as well as the microbiome of three neonates during their relapse. For one patient the same E. coli strain was found in blood and stool (this patient had no meningitis). For two patients microbiome analysis revealed a severe dysbiosis.

      Major comments:

      Although the authors announce in their title that they study E. coli that cause neonatal meningitis and in methods stipulate that they had a collection of 52 NMEC, we found in Supplementary Table 1, 29 strains (therefore most of the strains) isolated from blood and not CSF. This is a major limitation since only strains isolated from CSF can be designated with certainty as NMEC even if a pleiocytose is observed in the CSF. A very troubling data is the description of patient two with a relapse infection. As stated in the text line 225, CSF microscopy was normal and culture was negative for this patient! Therefore it is clear that patient without meningitis has been included in this study.

      We have reviewed the clinical data for our 52 NMEC isolates, noting that for some of the older Finish isolates we relied on previous publications. This data is shown in Table S1. To address the Reviewer’s comment, we have added the following text to the methods section (new text underlined).

      ‘The collection comprised 42 isolates from confirmed meningitis cases (29 cultured from CSF and 13 cultured from blood) and 10 isolates from clinically diagnosed meningitis cases (all cultured from blood).’

      Patient 2 was initially diagnosed with meningitis based on a positive blood culture in the presence of CSF pleocytosis (>300 WBCs, >95% polymorphs). We understand there may be some confusion with reference to a relapsed infection, which we now more accurately describe as recrudescent invasive infection in the revised manuscript.

      Another major limitation (not stated in the discussion) is the absence of clinical information on neonates especially the weeks of gestation. It is well known that the risk of infection is dramatically increased in preterm neonates due to their immature immunity. Therefore E. coli causing infection in preterm neonates are not comparable to those causing infection in term neonates notably in their virulence gene content. Indeed, it is mentioned that at least eight strains did not possess a capsule, we can speculate that neonates were preterm, but this information is lacking. The ages of neonates are also lacking. The possible source of infection is not mentioned, notably urinary tract infection. This may have also an impact on the content of VF.

      We agree. In the Discussion we now note the following (new text underlined):

      ‘… we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants.’

      Submission to Medrxiv, a requirement for review of our manuscript at eLife, necessitated the removal of some patient identifying information, including precise age and detailed medical history.

      Sequence analysis reveals the predominance of ST95 and ST1193 in this collection. The high incidence of ST95 is not surprising and well previously described, therefore, the concluding sentence line 132 indicating that ST95 E. coli should exhibit specific virulence features associated with their capacity to cause NM does not add anything. On the contrary, the high incidence of ST1193 is of interest and should have been discussed more in detail. Which specific virulence factors do they harbor? Any hypothesis explaining their emergence in neonates?

      We compared the virulence factors of ST95 and ST1193 and summarized this information in Figure 4. We also discussed how the K1 polysialic acid capsule in ST95 and ST1193 could contribute to the emergence of these STs in NM. Specifically, we stated the following: ‘We speculate this is due to the prevailing K1 polysialic acid capsule serotype found in ST95 and the newly emerged ST1193 clone [22, 37] in combination with other virulence factors [15, 28, 29] (Figure 4) and the immature immune system of preterm infants.’

      In the paragraph depicted the VF it is only stated that ST95 contained significantly more VF than the ST1193 strains. And so what? By the way "significantly" is not documented: n=?, p=?

      We compared the prevalence of known virulence factors between ST95 and ST1193, and showed that ST95 strains in our collection contained significantly more virulence factors than the ST1193 strains. The P-value and the statistical test used were included in Supplementary Figure 3. To address the reviewers concern, we have now also added this to the main manuscript text as follows (new text underlined):

      ‘Direct comparison of virulence factors between ST95 and ST1193, the two most dominant NMEC STs, revealed that the ST95 isolates (n = 20) contained significantly more virulence factors than the ST1193 isolates (n=9), p-value < 0.001, Mann-Whitney two-tailed unpaired test (Supplementary Table 1, Supplementary Figure 3).’

      The complete sequence of 18 strains is not clear. Results of Supplementary Table 2 are presented in the text and are not discussed.

      NMEC isolates that were completely sequenced in this study are indicated in bold and marked with an asterisk in Figure 1. This information is indicated in the figure legend and was provided in the original submission. All information regarding genomic island composition and location, virulence genes and plasmid and prophage diversity is included in Supplementary Table 2. This information is highly descriptive and thus we elected not to include it as text in the main manuscript.

      46 years is a very long time for such a small number of strains, making it difficult to put forward epidemiological or evolutionary theories. In the analysis of antibiotic resistance, there are no ESBLs. However, Ding's article (reference 34) and other authors showed that ESBLs are emerging in E. coli neonatal infection. These strains are a major threat that should be studied, unfortunately, the authors haven't had the opportunity to characterize such strains in their manuscript.

      We agree 46 years is a long time-span. The study by Ding et al examined 56 isolates comprised of 25 different STs isolated in China from 2009-2015, with ST1193 (n=12) and ST95 (n=10) the most common. Our study examined 58 isolates comprised of 22 different STs isolated in seven different geographic regions from 1974-2020, with ST1193 (n=9) and ST95 (n=20) the most common. Thus, despite differences in the geographic regions from which isolates in the two studies were sourced, there are similarities in the most common STs identified. The fact that we observed less antibiotic resistance, including a lack of ESBL genes, in ST1193 is likely due to the different regions from which the isolates were sourced. We acknowledged and discussed the potential of ST1193 harbouring multidrug resistance including ESBLs in our manuscript as follows:

      ‘Concerningly, the ST1193 strains examined here carry genes encoding several aminoglycoside-modifying enzymes, generating a resistance profile that may lead to the clinical failure of empiric regimens such as ampicillin and gentamicin, a therapeutic combination used in many settings to treat NM and early-onset sepsis [35, 36]. This, in combination with reports of co-resistance to third-generation cephalosporins for some ST1193 strains [22, 34], would limit the choice of antibiotic treatment.’

      Second part of the manuscript:

      The three patients who relapsed had a late neonatal infection (> 3 days) with respective ages of 6 days, 7 weeks, and 3 weeks. We do not know whether they are former preterm newborns (no term specified) or whether they have received antibiotics in the meantime.

      As noted above, patient ages were not disclosed to comply with submission to Medrxiv, a requirement for review of our manuscript at eLife.

      Patient 1: Although this patient had a pleiocytose in CSF, the culture was negative which is surprising and no explanation is provided. Therefore, the diagnosis of meningitis is not certain. Pleiocytose without meningitis has been previously described in neonates with severe sepsis. Line 215: no immunological abnormalities were identified (no details are given).

      We respectfully disagree with the reviewer. The diagnosis of meningitis is made unequivocally by the presence of a clearly abnormal CSF microscopy (2430 WBCs) and an invasive E. coli from blood culture. This does not seem controversial to the authors. We had believed it unnecessary to include this corroborative evidence, but have added the following to support our assertion:

      ‘The child was diagnosed with meningitis based on a cerebrospinal fluid (CSF) pleocytosis (>2000 white blood cells; WBCs, low glucose, elevated protein), positive CSF E. coli PCR and a positive blood culture for E. coli (MS21522).’

      On the contrary, the authors are surprised by the statement that CSF pleocytosis occurs in neonatal sepsis ‘without meningitis’ and do not know of any definitions of neonatal meningitis that are not tied to the presence of a CSF pleocytosis. Furthermore, the later isolation of E. coli from the CSF during the relapsed infection re-enforces the initial diagnosis.

      Patient 2: This patient had a recurrence of bacteremia without meningitis (line 225: CSF microscopy was normal and culture negative!). This case should be deleted.

      In a similar vein to the previous comment, we respectfully assert that this patient has clear evidence of meningitis (330 WBCs in the CSF, taken 24h after initiation of antibiotic treatment). In this case, molecular testing was not performed as, under the principle of diagnostic stewardship, it was not considered necessary by the clinical microbiologists and treating clinicians following the culture of E. coli in the bloodstream. We agree that this is not a case of recurrent meningitis, but our intention was to highlight the recrudescence of an invasive infection (urinary sepsis requiring admission to hospital and intravenous antibiotics) which we hypothesise has arisen from the intestinal reservoir. We did not state that all patients suffered from relapsed meningitis.

      Despite this, to address this reviewers concern, we have changed all reference to ‘relapsed infection’ to now read ‘recrudescent invasive infection’ in the revised manuscript.

      Patient 3: This patient had two relapses which is exceptional and may suggest the existence of a congenital malformation or a neurological complication such as abscess or empyema therefore, "imaging studies" should be detailed.

      This patient underwent extensive imaging investigation to rule out a hidden source. This included repeated MRI imaging of head and spine, CT imaging of head and chest, USS imaging of abdomen and pelvis and nuclear medicine imaging to detect a subtle meningeal defect and CSF leak. All tests were normal, and no abscess or empyema found.

      We have modified the text to include this information:

      Text in original submission: ‘Imaging studies and immunological work-up were normal.’

      New text in revised manuscript (underlined): ‘Extensive imaging studies including repeated MRI imaging of the head and spine, CT imaging of the head and chest, ultrasound imaging of abdomen and pelvis, and nuclear medicine imaging did not show a congenital malformation or abscess. Immunological work-up did not show a known primary immunodeficiency. At two years of age, speech delay is reported but no other developmental abnormality.’

      The authors suggest a link between intestinal dysbiosis and relapse in three patients. However, the fecal microbiomes of patients without relapse were not analysed, so no comparison is possible. Moreover, dysbiosis after several weeks of antibiotic treatment in a patient hospitalized for a long time is not unexpected. Therefore, it's impossible to make any assumption or draw any conclusion. This part of the manuscript is purely descriptive. Finally, the authors should be more prudent when they state in line 289 "we also provide direct evidence to implicate the gut as a reservoir [...] antibiotic treatment". Indeed the gut colonization of the mothers with the same strain may be also a reservoir (as stated in the discussion line 336). Finally, the authors do not discuss the potential role of ceftriaxone vs cefotaxime in the dysbiosis observed. Ceftriaxone may have a major impact on the microbiota due to its digestive elimination.

      We addressed the limitations of our study in the Discussion, including that we did not have access to urine or stool samples from the mother of the infants that suffered recrudescence, and thus cannot rule out mother-to-child transmission as a mechanism of reinfection. We have now added that we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants. The limitations of our study are summarised as follows in the Discussion (new text underlined):

      ‘This study had several limitations. First, our NMEC strain collection was restricted to seven geographic regions, a reflection of the difficulty in acquiring strains causing this disease. Second, we did not have access to a complete set of stool samples spanning pre- and post-treatment in the patients that suffered NM and recrudescent invasive infection. This impacted our capacity to monitor E. coli persistence and evaluate the effect of antibiotic treatment on changes in the microbiome over time. Third, we did not have access to urine or stool samples from the mother of the infants that suffered recrudescence, and thus cannot rule out mother-to-child transmission as a mechanism of reinfection. Finally, we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants.’

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      It would be useful to mention the sample size (number of genomes analysed, n=58) in the abstract to give readers a sense of the scale of the analysis.

      We have added the number of genomes in the abstract as suggested (new text underlined).

      ‘Here we investigated the genomic relatedness of a collection of 58 NMEC strains spanning 1974-2020 and isolated from seven different geographic regions.’

      The term 'strain' is used throughout, it would be clearer to use 'isolates' to describe the biological material and 'genomes' when the unit being referred to is genome sequences. For example, lines 108-111 use 'strain' to mean the collection of 52 isolates but also uses 'strain' to mean the collection of 58 genomes including those of the 52 isolates that the authors sequenced plus a further 6 genomes of isolates that they do not have in their isolate collection.

      We have changed the term ‘strain’ to ‘isolate’ or ‘genome’ as suggested.

      Figure 1 (annotated phylogeny) is hard to read and interpret, as so much data is presented. It would assist readers if the authors could provide an interactive form of the phylogeny and metadata/genomic feature data discussed in the text, e.g. using microreact.org, so that details can be explored more easily.

      This is an excellent suggestion, and we created a project on microreact.org. This information has been added to the Figure 1 legend.

      https://microreact.org/project/oNfA4v16h3tQbqREoYtCXj-high-risk-escherichia-coli-clones-that-cause-neonatal-meningitis-and-association-with-recrudescent-infection.

      It would be useful to provide information on the frequency and/or distribution of the virulence factors in the broader E. coli population, to provide context for readers and to better understand the importance/significance of the high frequency of the reported virulence factors within NMEC.

      As noted above, we agree the prevalence of virulence factors in our collection is interesting. We discussed the prevalence of these virulence factors in our collection, and the detailed data is presented in Table S1. However, we also note a limitation in our study is the number of isolates, and thus we would prefer to avoid evaluation of the prevalence of these virulence factors in the context of a broader E. coli population. There are other studies that have examined NMEC virulence factors in the past; some examples are noted below, and we have now referenced these in our manuscript (note Ref 15 was suggested by Reviewer 3 in a comment below; PMID: 11920295).

      Ref 15: Johnson JR, Oswald E, O'Bryan TT, Kuskowski MA, Spanjaard L. Phylogenetic distribution of virulence-associated genes among Escherichia coli isolates associated with neonatal bacterial meningitis in the Netherlands. J Infect Dis 2002; 185(6): 774-84.

      Ref 28: Wijetunge DS, Gongati S, DebRoy C, et al. Characterizing the pathotype of neonatal meningitis causing Escherichia coli (NMEC). BMC Microbiol 2015; 15: 211.

      Ref 29: Bidet P, Mahjoub-Messai F, Blanco J, et al. Combined Multilocus Sequence Typing and O Serogrouping Distinguishes Escherichia coli Subtypes Associated with Infant Urosepsis and/or Meningitis. J Infect Dis. 2007; 196(2):297-303.

      I suggest avoiding the term 'global' to describe the collection, given that there are only seven countries included in the collection and two of the most populous continents (Africa and South America) are not represented at all.

      We agree, and now refer to our collection as ‘an NMEC strain collection from geographically diverse locations.’

      Reviewer #2 (Recommendations For The Authors):

      This is a suggestion regarding discussion/food for thought: This study sheds information on genomic features and indicates the presence of a reservoir in the infected infant. Previous studies have demonstrated the presence of a reservoir in the vaginas of women with recurrent UTIs. Is there any information as to whether the mothers of these infants, especially the three with recrudescent infection, had a UTI or recurrent UTI in their life? It may be worthwhile discussing the potential of testing for E. coli in expecting mothers, if they have a history of UTI.

      We do not have such data, and as indicated above we note this as a limitation of our study.

      It is unclear as written in the main text, as to whether all three cases of recrudescent infection come from the same geographical location. It would be easier to have this information in the corresponding main text, in addition to the supplement.

      The three cases of recrudescent invasive infection were from 3 different locations. We have added the information as following (new text underlined):

      ‘These patients were from different regions in Australia.’

      Reviewer #3 (Recommendations For The Authors):

      Line 48 and 67 change the word "devasting".

      Changed as suggested.

      Line 49 second most in full-term infants.

      Changed as suggested.

      Line 56 delete the sentence "antibiotic resistance genes occurred infrequently".

      We changed the sentence, which now reads (new text underlined):

      ‘Antibiotic resistance genes occurred infrequently in our collection’.

      Line 76 reference 10 is inappropriate.

      Reference 10 reported that 5/24 infants treated for neonatal Gram-negative bacillary meningitis over a 10-year period had a relapse of meningitis after the initial course of treatment. Four of the isolates that caused these relapsed infections were E. coli.

      To address the reviewers concern, we have altered the text as follows (new text underlined):

      ‘Moreover, NMEC is an important cause of relapsed infections in neonates [10]’.

      Line 83 several references related to serotypes are missing, notably doi.org/10.1086/339343.

      We have added this reference.

      Line 171 significantly? n=?, p=?

      The numbers and P-value were provided in the Supplementary Figure 3 legend. We have now added these to the text as follows:

      ‘Direct comparison of virulence factors between ST95 and ST1193, the two most dominant NMEC STs, revealed that the ST95 isolates (n = 20) contained significantly more virulence factors than the ST1193 isolates (n = 9); P-value < 0.001, Mann-Whitney two-tailed unpaired test (Supplementary Table 1, Supplementary Figure 3).”

      Figure 4 is not necessary.

      We respectfully disagree. Figure 4 provides an illustrative comparison of virulence factors between the two most dominant NMEC sequence types, ST95 and ST1193. We believe this will be informative for many readers.

      Line 311 "We speculate....of preterm infants" This sentence does not add anything to the discussion.

      We respectfully disagree and have kept the sentence. This reflects our opinion.

      Line 320 "clear clinical risk factors to explain... ». Term of neonates is missing.

      Updated as follows (new text underlined):

      ‘Although reported rarely, recrudescent invasive E. coli infection in NM patients, including several infants born pre-term, has been documented in single study reports [39, 40]. In these reports, infants received appropriate antibiotic treatment based on antibiogram profiling and no clear clinical risk factors to explain recrudescence were identified, highlighting our limited understanding of NM aetiology.’

    1. n most cases, there are two kinds of errors in the Vietnamese language:mistyped errors and misspelled errors [11]. Mistyped errors are errors that occurduring the typing process. The majority of these mistakes are caused by the

      Có 2 loại lỗi phổ biến: - Lỗi đánh máy sai:là các lỗi gõ sai chữ trong quá trình đánh máy. Chỉ dừng ở mức âm tiết. Có thể chia thành 2 loại lỗi là: lỗi từ giả và lỗi từ thật. Lỗi từ thật là khi xảy ra lỗi thì từ lỗi đó lại có trong từ điển. Lỗi từ giả thì ngược lại. - Lỗi phát âm sai là lỗi đánh sai về phát âm ( lỗi d-r, l-n, ...)

    1. their gender, race, age, class, and so on are not specified. If we shift to an intersectional framework, one of the implications is that we must restructure testing at all stages, from early prototypes through quality control in mass production, around what Algorithmic Justice League founder Joy Buolamwini has described as intersectional benchmarks

      La perspectiva inter seccional ayuda a asumir los problemas de discriminación y dominación. Es bueno revisar lo que hace la fundación Liga de Justicia Algorítmica. ¿Qué ocurre si las investigaciones que quiero implementar no les interesa esta perspectiva? ¿Qué aporta esta perspectiva a los diseños metodológicos y las perspectivas teóricas en las investigaciones cuyo objeto no es poner de manifiesto las relaciones de poder o las desigualdades estructurales?

    2. wever, in practice this approach also leads to the reproduction and reification of existing social categories through algorithmic surveillance, tracking users across sites, gathering and selling their data, and the development of filter bubbles (only showing users content that we believe they are comfortable with).

      Uno de los problemas fundamentales de la justicia es la reificación o los procesos de reconocimiento. Tal vez estos pasan, también por un asunto que tradicionalmente se ha considerado menor, el diseño.

    3. Now, imagine auditing the same admissions algorithm, but under the assumptions of algorithmic justice. This approach is concerned not only with individualized symmetrical treatment, but also with the individual and group-level effects of historical and ongoing oppression and injustice within the matrix of domination, as well as how to ultimately produce a more just distribution of benefits, opportunities, and harms across all groups of people. In our example, this means that the algorithm designers must discuss, debate, and decide upon what they believe to be a just distribution of outcomes.

      ¿Cuál es el tránsito entre diseño injusto , injusticia algoritmica, diseño justo y justicia algorítmica? ¿Qué es lo injusto o lo justo en cada uno de estos? ¿En qué reside su injusticia? ¿En la reproducción de desigualdades en raza, clase, género, estatus migratorio, condición de ciudadanía, etc? ¿La injusticia tiene que ver solo con la libertad o con el ejercicio y toma de decisiones sobre lo común?

    4. g of racial, gender, disability, economic, environmental, and decolonial justice

      ¿Cómo es esta justicia? ¿Hay criterios específicos para cada uno de estos? ¿Hay criterios generales o universales trasversales a todos estos? Revisemos el orden: raza, género, capacidad, economía, ambiental, decolonial. ¿Qué otros se les puede aumentar, sumar? ¿Cuál es la noción de justicia que está aquí a la base? ¿Teoría de la justicia distributiva? ¿Justicia basada en la libertad o distribución de la libertad? ¿Noción utilitarista de la justicia?

    5. tivist use of Facebook as a tool to help organize political protests is a story that has been widely told in both scholarly and popular writing. The best of these accounts complicate any simplistic narrative about the relationship between social media platforms and political protest activity.

      Uso de Facebook, X y Mastodont para organizar la protesta política por parte de movilizaciones sociales y grupos de personas que protesta. La relación entre medios de comunicación, plataformas y activismo político de protesta es compleja, ¿qué tanto hay una sobre determinación por parte de los dispositivos, las plataformas como facebook o x a las protestas, movilizaciones y movimientos sociales en lo que se refiere a su organización, formas de toma de decisiones, representación, etc.

    6. In design justice, by contrast, values stem from the lived experience of communities and individuals who exist at the intersection of systems of structural oppression and resistance.

      Este principio es importante, "los valores de la experiencia vivida de comunidades e individuos, que existen en la intersección entre sistemas estructurales de opresión y resistencia". Opresión y resistencia. ¿Cómo son los aprendizajes de estas comunidades e individuos si tradicionalmente no son los que escriben artículos y libros de investigación o textos que circulan en la academia? Trabajar con ellos IAP, teatro del oprimido. Pero, lo más importante es tener la sensibilidad para asumir los retos en la investigación que hagamos, sin importar si no aplicamos esta metodología. ¿En qué consiste la perspectiva crítica, qué es lo crítico en esos sentidos?

    7. Tampoco la señal perceptiva de un icono de disquete ubicado al lado del La opción Guardar en un menú desplegable ayuda a alguien que nunca ha usado un disquete el disco entiende la asequibilidad que se ofrece, al menos hasta que lo hayan hecho aprendió lo que significa.

      Las plataformas digitales han revolucionado el comercio minorista, conectando a consumidores y organizaciones en ecosistemas interactivos. Estas plataformas desempeñan un papel crucial en la actualidad. Permíteme explicarte por qué Facebook y otras plataformas similares son esenciales para las organizaciones minoristas, puesto que permite visibilidad y alcance, Facebook es una herramienta que se ha vuelto poderosa para crear y mantener una presencia en línea. Las organizaciones o grupos minoritarios pueden llegar a un público masivo y diverso a través de esta página o de otras que cuenten con usuarios o también llamados seguidores. Estas plataformas permiten interactuar con usuarios que siguen el tipo de contenido que ofrecen las organizaciones o grupos, lo que aumenta la visibilidad de la marca.

    8. asistentes virtuales Siri, Cortana, Google Assistant y S Voice eran capaces de responder a preguntas sobre qué hacer en caso de un ataque cardíaco o pensamientos suicidas, pero ninguno reconocía las frases “He "He sido violada" o "he sido agredida sexualmente", 40 a pesar de las altas tasas de violación, agresión sexual y violencia de pareja experimentadas por mujeres y femmes

      En este caso, se evidencia que configuran estas herramientas para el uso de conocimiento más no para generar una acción en la persona.

      Una de los metodos de mercadeo de Apple con sus relojes es la inactividad de la persona para enviar una señal.

      Description

    9. Put another way, why do we continue to design technologies that reproduce existing systems of power inequality when it is so clear to so many that we urgently need to dismantle those systems? What will it take for us to transform the ways that we design technologies (sociotechnical systems) of all kinds, including digital interfaces, applications, platforms, algorithms, hardware, and infrastructure, to help us advance toward liberation?

      Este tipo de preguntas lleva a problematizar o desvelar el carácter político que se esconde también en las plataformas e infraestructuras tecnológicas, enteniendo lo político también con las acciones y decisiones que operan y condicionan el marco de lo real.

    10. First, though, five of the protest organizers, each from a diverse intersection of queer, trans*, and other identities—Black, Latinx, Asian, immigrant, Disabled working-class—pass a microphone around and read a collective statement about the reasons for the mobilization:

      Llama la atención el caso de Javier Milei en Argentina y la "depuración" de gran número de mininsterios, cada uno de los cuales responde a un lucha social en el marco histórico. O la recién prohibición del uso del lenguaje inclusivo en comunicados oficiales, como si el lenguaje se pudiera vetar. Antes que superarse el estilo Trump, pareciera ganar cada vez más adeptos en el Latinoamérica, como se evidencia, además, con el gran respaldo que Bolsonaro tiene en Brasil o con la reelección de Bukele en El Salvador.

    11. a justicia del diseño pregunta si las posibilidades de un objeto o sistema diseñado reducen desproporcionadamente las oportunidades para grupos de personas ya oprimidos al tiempo que mejoran las oportunidades de vida de los grupos dominantes, independientemente de si los diseñadores pretenden este resultado.

      Definición del Diseño justo

    12. ¿Por qué el tiempo, la energía y la brillantez de tantos diseñadores, desarrolladores de software, gerentes de productos y otras personas que trabajan en plataformas se centran en optimizar nuestro mundo digital para captar y monetizar nuestra atención, en lugar de otros objetivos potenciales (por ejemplo, maximizar el compromiso cívico, ¿Tomar decisiones ambientalmente sostenibles, generar empatía o lograr cualquiera de los casi infinitos resultados deseables alternativos)?

      Para qué la tecnología fuera del campo del lucro?

    13. Académicos de la comunicación Moya Z. Bailey, Sarah Jackson y Brooke Foucalt-Welles analizan cómo las redes de movimiento social aproveche las posibilidades de Twitter en campañas de activismo hashtag como #SayHerName, #GirlsLikeUs y #MeToo.7

      La presencia investigativa de profesionales de la comunicación demuestra lo significativo y evidente de la inmediatez y eficacia de los hashtag, que llegan y hacen ruido en los procesos de comunicación entre los usuarios, seguidores o investigadores sobre temas relevantes o llamativos.

    14. Escobar se basa en décadas de trabajo con movimientos sociales liderados por pueblos indígenas y afrodescendientes de América Latina y el Caribe para argumentar diseño autónomo. Rastrea las formas en que más diseña los procesos de hoy están orientados hacia la reproducción de la “one world” ontología. Esto significa que la tecnología se utiliza principalmente para extenderse la modernidad patriarcal capitalista y los objetivos del mercado y/o el estado, y para borrar las formas indígenas de ser, conocer y hacer (ontologías, epistemologías, prácticas y mundos de vida). Escobar argumenta para un enfoque descolonizado del diseño que se centra en la colaboración y prácticas basadas en el lugar y que reconocen la interdependencia de todos personas, seres y la tierra. Insiste en la atención a lo que llama la dimensión ontológica del diseño: todo diseño reproduce ciertas formas de ser, conocer y hacer. Está interesado en el concepto zapatista de crear “un mundo donde encajan muchos mundos,”110en lugar de la “one world” proyecto de globalización neoliberal.

      El pensamiento ontológico de Escobar se nutre de argumentos de Freire y Fals Borda, en donde la comunicación se puede interpretar como una acción participación que da respuesta a sentimientos, emociones, prácticas colaborativas de grupos vulnerados, y en donde se reconoce su accionar político-transformador.

    15. Por qué las plataformas de redes sociales más populares proporcionan tan limitado affordances para el importante trabajo de organización y movimiento comunitario ¿edificio? Por qué es el tiempo, la energía y el brillo de tantos diseñadores, desarrolladores de software, gerentes de productos y otros que trabajan en plataformas enfocado en optimizar nuestro mundo digital para capturar y monetizar nuestro atención, sobre otros objetivos potenciales (por ejemplo, maximizar lo cívico compromiso, tomar decisiones ambientalmente sostenibles, construir empatía, o lograr cualquiera de alternativa casi infinita deseable ¿resultados)? Dicho de otra manera,por qué seguimos diseñando tecnologías que reproducen los sistemas existentes de desigualdad de poder cuando está tan claro ¿a tantos que necesitamos urgentemente desmantelar esos sistemas? Qué será nos lleva transformar las formas en que diseñamos las tecnologías (sistemas sociotécnicos) de todo tipo, incluidas las interfaces digitales, aplicaciones, plataformas, algoritmos, hardware e infraestructura, para ¿ayudarnos a avanzar hacia la liberación?

      ¿En este desarrollo de infraestructura digital, qué papel juega el software libre?, ¿qué desafíos presenta?

    16. Para muchos, la “revelación” no deseada de una SOGI no hetero y/o cis normativa puede tener consecuencias desastrosas en el mundo real, que van desde burlas, intimidación y violencia emocional y física por parte de pares hasta la pérdida de la familia, la inestabilidad de la vivienda y la negación de la vivienda.

      La importancia del mundo real al mundo virtual en redes sociales

    17. Las posibilidades de un objeto nunca son igualmente perceptibles para todos ni nunca están igualmente disponibles para todos; una prestación determinada siempre es más perceptible, más disponible, o ambas cosas, para algunos tipos de personas.

      El desarrollo de la tecnología esta pensada para las personas "sin ningún tipo de discapacidad" pero desafortunadamente en la sociedad estas herramientas llegan a todo tipo de personas.

    18. La perceptibilidad de la asequibilidad también suele diferir para las personas daltónicas, ciegas o con discapacidad visual, o para las personas sordas o con problemas de audición. Por tanto, el punto de vista determina si una prestación es perceptible en absoluto para un usuario determinado, y la perceptibilidad de la prestación siempre está determinada por el punto de vista (ubicación dentro de la matriz de dominación); cada posibilidad es más perceptible para algunos tipos de usuarios que para otros.

      Aquí podemos entender la situación sobre la alfabetización sistematica. Es decir, cuando no se conoce las funciones o metodos que trabaja alguna herramienta, el ser humano no podra aplicarla de la mejor manera.

    Annotators

    Annotators

    1. Character allByteCharacters.

      Al ejecutar este código genera como resultado:

      El resultado obtenido quiere decir que permite “imprimir” o ejecutar los 256 caracteres del código extendido ASCII. Sin embargo, se ejecuta palabras o caracteres sin sentido. Este error se da probablemente porque puede haber un problema de visualización de los símbolos latinos o romanos desde el sistema operativo.

      Por lo tanto, que un carácter no sea imprimible dentro del Glamorous Toolkit, NO quiere decir que, no se pueda ver cuando se exporta a otros entornos, por ejemplo a sitios web.

    2. [:x | x+2] value: 20. b := [:x | x+2]. b value: 20.

      [:x | x+2] value: 20. * Este código crea un bloque directamente en el lugar donde se necesita y lo ejecuta inmediatamente con el argumento 20. El bloque toma x como argumento, suma 2 a x y devuelve el resultado. En este caso, se pasa 20 el resultado será 20 + 2 = 22

      b := [:x | x+2]. b value: 20. * primero se crea un bloque y se asigna a la variable b. Luego, el bloque almacenado en b se ejecuta con el argumento 20. Este enfoque permite reutilizar el mismo bloque en múltiples lugares o en momentos diferentes dentro del código

    3. Bloques For this part a Basic understanding of Basic Types is recommended. If you have not done that part yet, please go to that subtree and run the code there Ahora hablemos de los bloques. Piensa en los bloques como una manera de 'congelar' código que luego podremos ejecutar por demanda, cuando queramos y/o las condiciones para su ejecución se cumplan. Los bloques son métodos anónimos, lo cual quiere decir que no es necesario ponerles nombres para invocarlos (como ocurre con las operaciones sobre objetos que hemos visto hasta el momento) y pueden pueden ser almacenados en variables. Los bloques están delimitados por paréntesis cuadrados: []
      • Métodos anónimos: Los bloques no tienen nombres asociados y pueden ser creados y utilizados sobre la marcha sin necesidad de definir un nombre específico para ellos.

      • Almacenamiento en variables: Los bloques pueden ser asignados a variables y pasados como argumentos a otros métodos o bloques.

      • Delimitados por paréntesis cuadrados: Los bloques en Pharo están delimitados por paréntesis cuadrados [ ].

      • Captura de contexto: Los bloques pueden capturar variables definidas en el contexto en el que se crean, lo que les permite acceder y manipular esos valores

    4. Prioridad Los mensajes unarios son ejectuados primero, los mensajes binarios son ejecutados despues y finalmente las cadenas de mensajes: paréntesis > Unary > Binary > Keywords

      En esta sección tenemos:

      • Paréntesis: Las expresiones dentro de paréntesis se evalúan primero.
      • Mensajes unarios: Los mensajes unarios, que consisten en un solo identificador, se evalúan después de las expresiones entre paréntesis.
      • Mensajes binarios: Los mensajes binarios, que consisten en operadores como +, -, *, etc., se evalúan después de los mensajes unarios.
      • Mensajes de palabra clave: Los mensajes de palabra clave, que consisten en uno o más identificadores seguidos de dos puntos y un argumento, se evalúan después de los mensajes binarios
    5. Binario

      En esta sección los "mensajes binarios" son aquellos que se envían a un objeto junto con otro objeto, sin palabras clave o métodos especiales entre ellos. La forma típica de un mensaje binario es la siguiente

      anObjecto aMessage anotherObject

    6. La concatenación de String usa el operador coma: ['PharoTutorial', ' is cool']. "versión cambiada" 'Pharo tutorial ', ' is cool', ' when i active the code '

      La concatenación de cadenas (strings) es el proceso de unir dos o más cadenas para formar una sola cadena más larga y se realiza utilizando el operador coma

      Ejemplo: 'Pharo tutorial ', ' is cool', ' when i active the code '

    1. Author Response

      Reviewer #1 (Public Review):

      The author's goal was to determine the role of O-GlcNAc modification in associate learning in Drosophila using an odor discriminatory task. In particular, they sought to determine the population of O-GlcNAc modified proteins in a region of the brain critical for memory, the mushroom body. They provide compelling evidence that there are brain-region-specific populations of O-GlcNAc modified proteins and that in the mushroom body, proteins involved in translation represent a sizable, and larger fraction than elsewhere in the central nervous system. Using expression of a bacterial protein that cleaves O-GlcNAc in the mushroom body, they show both reductions in the levels of this modification and effects on associative learning. Further exploration of new protein synthesis in situ supports the hypothesis that O-GlcNAc modification affects the activity of the translational machinery and could provide the basis for learning deficits when O-GlcNAc levels are compromised. Rescue of deficits resulting from reductions in O-GlcNAc was achieved by over-expression of dMyc, a known regulator of ribosome biogenesis and translation. While the critical role of protein synthesis in learning is long established, and that O-GlcNAc modification regulates protein synthesis, this work connects O-GlcNAc modification in a specialized region of the brain to translation regulation and associative learning. The authors also provide a method for identification of O-GlcNAc modified proteins using a tissue-specific and inducible proximity-labelling method. This will provide a useful tool for further functional studies of O-GlcNAc modification.

      Thank you for summarizing our main findings and recognizing the usefulness of the tool reported here.

      Reviewer #2 (Public Review):

      In this report Yu et al. try to demonstrate how O-GlcNAcylation of ribosomal proteins in the mushroom body (MB) is required for protein synthesis and olfactory learning. The authors develop a new method combining the O-GlcNAc binding activity of an OGlcNAcase (OGN) and TurboID for efficient isolation. This novel method is a useful tool for the identification of O-GlcNAc modified proteins and closely interacting partners. Transgenic expression of this binder allows the authors to perform a profiling that can be time and tissue/region/cell specific. This novel tool is thoroughly tested to show it works in cultured cells, whole Drosophila and in a tissue specific manner expressing it pan-neuronally or specific regions of the brain.

      The authors had previously shown that reduced O-GlcNAcylation through transgenic expression of a highly active OGN affected olfactory learning. In this work the same approach is used to reduce O-GlcNAcylation in different brain regions to show that specific reduction in the adult MB reduced olfactory learning performance. As control OGN expression in the ellipsoid body has no effect on olfactory learning. Optic and antennal lobes could not be tested as OGN expression affected olfactory acuity. The most critical part of this finding is time specific expression of OGN in the adult in a tissue specific manner given the developmental defects it induces with earlier expression. The MB has a widely reported role in associative learning, therefore this finding while not unexpected it is satisfying.

      Thank you for recognizing the significance of our work.

      Yu et al. use their TurboID-OGA to identify O-GlcNAcylated proteomes in different brain regions. The authors focus on the MB given its role in associative learning and the effect of reduced O-GlcNAcylation in this region. Among other substrates several ribosomal proteins are found to be specifically O-GlcNAcylated to a greater extent in the MB compared to other brain regions.

      To demonstrate the role of MB O-GlcNAcylated ribosomes in protein synthesis an ex vivo OPP fluorescent assay is used in brains of flies expressing OGN or a mutant form lacking its catalytic and binding activities. The experiment shows reduced protein synthesis in the MB. In addition, the authors can increase protein synthesis inducing ribosomal biogenesis through the expression of dMyc. Flies expressing of dMyc and OGN together do not present the learning deficits of flies carrying only OGN. Protein synthesis in MB has been previously reported to be required for associative learning (for example Wu et al.2017 or Lin et al. 2022) and the present results bring further support. A link between ribosomal O-GlcNAcylation and protein synthesis could be a really interesting finding but, unfortunately the experiments presented in this work are still too preliminary.

      The experiments presented just focus on ribosomal proteins while these are just some of the O-GlcNAcylation substrates in the MB. While a correlation between ribosomal modification and protein synthesis is shown, a demonstration is not provided. Many other mechanisms and O-GlcNAcylation of other substrates could account for the same observations. For example, O-GlcNAcylation has been reported to have a role in protein synthesis affecting different translation initiation factors (Li et al 2018, Shu et al 2022). In vitro experiments where specific O-GlcNAcylation ribosomal components could be targeted are required. In addition, O-GlcNAcylation is also known to modify ribosomal-associated mRNAs. Experiments where specific mutations preventing O-GlcNAcylation in ribosomes could demonstrate a direct link of such ribosomal modifications in olfactory learning.

      We appreciate that you bring up a crucial point that our data fall short for a causal connection between O-GlcNAcylation of ribosomes and translational activity. We have made significant changes to the text throughout the manuscript to make our description more accurate.

    2. Reviewer #1 (Public Review):

      The author's goal was to determine the role of O-GlcNAc modification in associate learning in Drosophila using an odor discriminatory task. In particular, they sought to determine the population of O-GlcNAc modified proteins in a region of the brain critical for memory, the mushroom body. They provide compelling evidence that there are brain-region-specific populations of O-GlcNAc modified proteins and that in the mushroom body, proteins involved in translation represent a sizable, and larger fraction than elsewhere in the central nervous system. Using expression of a bacterial protein that cleaves O-GlcNAc in the mushroom body, they show both reductions in the levels of this modification and effects on associative learning. Further exploration of new protein synthesis in situ supports the hypothesis that O-GlcNAc modification affects the activity of the translational machinery and could provide the basis for learning deficits when O-GlcNAc levels are compromised. Rescue of deficits resulting from reductions in O-GlcNAc was achieved by over-expression of dMyc, a known regulator of ribosome biogenesis and translation. While the critical role of protein synthesis in learning is long established, and that O-GlcNAc modification regulates protein synthesis, this work connects O-GlcNAc modification in a specialized region of the brain to translation regulation and associative learning. The authors also provide a method for identification of O-GlcNAc modified proteins using a tissue-specific and inducible proximity-labelling method. This will provide a useful tool for further functional studies of O-GlcNAc modification.

    3. Reviewer #2 (Public Review):

      In this report Yu et al. try to demonstrate how O-GlcNAcylation of ribosomal proteins in the mushroom body (MB) is required for protein synthesis and olfactory learning. The authors develop a new method combining the O-GlcNAc binding activity of an OGlcNAcase (OGN) and TurboID for efficient isolation. This novel method is a useful tool for the identification of O-GlcNAc modified proteins and closely interacting partners. Transgenic expression of this binder allows the authors to perform a profiling that can be time and tissue/region/cell specific. This novel tool is thoroughly tested to show it works in cultured cells, whole Drosophila and in a tissue specific manner expressing it pan-neuronally or specific regions of the brain.

      The authors had previously shown that reduced O-GlcNAcylation through transgenic expression of a highly active OGN affected olfactory learning. In this work the same approach is used to reduce O-GlcNAcylation in different brain regions to show that specific reduction in the adult MB reduced olfactory learning performance. As control OGN expression in the ellipsoid body has no effect on olfactory learning. Optic and antennal lobes could not be tested as OGN expression affected olfactory acuity. The most critical part of this finding is time specific expression of OGN in the adult in a tissue specific manner given the developmental defects it induces with earlier expression. The MB has a widely reported role in associative learning, therefore this finding while not unexpected it is satisfying.

      Yu et al. use their TurboID-OGA to identify O-GlcNAcylated proteomes in different brain regions. The authors focus on the MB given its role in associative learning and the effect of reduced O-GlcNAcylation in this region. Among other substrates several ribosomal proteins are found to be specifically O-GlcNAcylated to a greater extent in the MB compared to other brain regions.

      To demonstrate the role of MB O-GlcNAcylated ribosomes in protein synthesis an ex vivo OPP fluorescent assay is used in brains of flies expressing OGN or a mutant form lacking its catalytic and binding activities. The experiment shows reduced protein synthesis in the MB. In addition, the authors can increase protein synthesis inducing ribosomal biogenesis through the expression of dMyc. Flies expressing of dMyc and OGN together do not present the learning deficits of flies carrying only OGN. Protein synthesis in MB has been previously reported to be required for associative learning (for example Wu et al.2017 or Lin et al. 2022) and the present results bring further support. A link between ribosomal O-GlcNAcylation and protein synthesis could be a really interesting finding but, unfortunately the experiments presented in this work are still too preliminary.

      The experiments presented just focus on ribosomal proteins while these are just some of the O-GlcNAcylation substrates in the MB. While a correlation between ribosomal modification and protein synthesis is shown, a demonstration is not provided. Many other mechanisms and O-GlcNAcylation of other substrates could account for the same observations. For example, O-GlcNAcylation has been reported to have a role in protein synthesis affecting different translation initiation factors (Li et al 2018, Shu et al 2022). In vitro experiments where specific O-GlcNAcylation ribosomal components could be targeted are required. In addition, O-GlcNAcylation is also known to modify ribosomal-associated mRNAs. Experiments where specific mutations preventing O-GlcNAcylation in ribosomes could demonstrate a direct link of such ribosomal modifications in olfactory learning.

    1. Check out this great interactive Timeline of Learning Theories c/o MyBrainisOpen

      This is a really useful resource that summarises and lists a lot of the major learning theories I've studied in other classes, I'll come back to this when referencing.

    1. h contro- ‘versal, i important tothe efficacy of interna tional human rights law, for i¢ purports co impose obligations on nations that have not fully embraced human cights treaties.

      customary int'l law is important because it acts as an enforcer of int'l law o EVERY nation

    1. How has the dejection come to you at this juncture? This is not fit for a person of noble mind and deeds. It is disgraceful, and it does not lead one to heaven, O Arjuna.

      Krishna's admonishment of Arjuna highlights the importance of duty and righteousness, urging Arjuna to rise above his emotional turmoil.

    1. El presidente entra y sale del mundo virtual. Un sitio mide en Internet sus horas de estancia en la red X. A veces más de cuatro. Podría chatear o comunicarse con su novia. Pero parece que no. El teléfono le abre la puerta a una segunda vida en las noches de insomnio. X es su Tron temporal y acaso ese acostumbramiento a la virtualidad el que le permite la fantasía de un curioso bilingüismo. No hablamos del inglés sino del hebreo. Postea en la lengua semítica, acaso con ayuda de un rabino o de algún programa de traducción. Lo que importa finalmente es el resultado.

      Twitter (X) es el Tron temporal de Milei.

  3. inst-fs-iad-prod.inscloudgate.net inst-fs-iad-prod.inscloudgate.net
    1. O UR FRIENDSHIP CAME ALL AT ONCE AFTER THAT, LIKE spring floods from themountains. Before, the boys and I had imagined that his days were filledwith princely instruction, statecraft and spear. But I had long since learnedthe truth: other than his lyre lessons and his drills, he had no instruction.One day we might go swimming, another we might climb trees. We madeup games for ourselves, of racing and tumbling. We would lie on the warmsand and say, “Guess what I’m thinking about.”

      yess friendship montage

    2. O NE AFTERNOON, as I went to leave him to his private drills he said, “Whydon’t you come with me?” His voice was a little strained; if I had notthought it impossible, I might have said he was nervous. The air, which hadgrown comfortable between us, felt suddenly taut

      actually patro might be his first friend in a way

    1. Texto fundamental da filosofia contemporânea, Diferença e Repetição, de Gilles Deleuze, afirma o pensar como um acontecimento desconfortável, mas fascinante

      reflectir sobre o conceito de diferença e repetição na filosofia de Deleuze e relacionar com o visionamento do filme

    1. the danger of sophia without phronesis

      Es un peligro creer que uno sabe mucho si no ha comprobado en la práctica si sabe o no aplicarlo correctamente. Ese tipo de conocimiento solo alimenta al ego. Puede llevarnos al orgullo y la presunción. A cometer errores ya que damos por sentado que sabemos algo cuando no lo hemos experimentado realmente en la vida real.

    1. En las últimas décadas, los biólogos evolutivos han mejorado enormemente los métodos computacionales para agilizar la recopilación y el análisis de datos genéticos de sistemas no modelo. Sin embargo, las herramientas para datos fenotípicos están rezagadas a pesar de la necesidad crítica de dichos datos para comprender cómo han evolucionado los rasgos a escalas micro y macroevolutivas. En comparación con los datos de las bases de datos genéticas estandarizadas (NCBI, etc.), los datos fenotípicos a menudo se encuentran dispersos en repositorios no estándar (por ejemplo, material complementario), no están disponibles públicamente o no son comparables entre estudios debido a la subjetividad de los términos utilizados. incapacidad para probar la homología dados los datos faltantes y variabilidad de los enfoques para codificar caracteres y estados de caracteres. La terminología subjetiva para caracterizar fenotipos obstaculiza nuestra capacidad de aprovechar los datos existentes para metanálisis a gran escala en investigaciones evolutivas o morfológicas o determinar si los resultados de los estudios son comparables. Estos problemas se magnifican en estudios que incluyen morfologías complejas o mal caracterizadas donde la terminología es a menudo imprecisa y conflictiva, o específica del grupo de estudio. Para aumentar la claridad de los datos y la reproducibilidad científica, abogamos por el uso de ontologías existentes y la mejora continua de las ontologías vegetales.

      TO DO - Leer [ ]

    1. Author Response

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

      Reviewer #1 (Public Review):

      Major Concerns:

      (1) An important point that the authors should clarify in this study is whether mice are detecting qualitative or quantitative differences between fresh and old cat saliva. Do the environmental conditions in which the old saliva was maintained cause degradation of Fel d 4, the main protein known for inducing a defensive response in rodents? (see Papes et al, 2010 again). If that is the case, one would expect that a lower concentration of Fel d 4 in the old saliva after protein degradation would result in reduced antipredator responses. Alternatively, if the authors believe that different proteins that are absent in the old saliva are contributing to the increased defensive responses observed with the fresh saliva, further protein quantification experiments should be performed. An important experiment to differentiate qualitative versus quantitative differences between the two types of saliva would be diluting the fresh saliva to verify if the amount of protein, rather than the type of protein, is the main factor regulating the behavioral differences.

      We thank the reviewer for their important suggestions. We agree that both the quality and quantity of molecular components in saliva undergo changes after the saliva is kept at room temperature for 4 hours. Our findings indicate that mice detect these changes through the VNO and adjust their defensive response patterns accordingly. For instance, freezing behavior is reduced in response to 4-hour-old saliva compared to fresh saliva. On the other hand, the duration of interaction with saliva (investigation behavior) remains low, and the stress hormone ACTH level is upregulated in both cases. A future study ought to identify the specific molecules—most likely proteins or peptides—in cat saliva responsible for these distinct defensive responses in mice. While Fel d 4 stands as one of the potential candidates as it has been shown to induce a form of defensive behavior in mice (Papes et al., 2010), there exists a possibility of a different molecule or a combination of multiple molecules playing a role. Once the molecules are identified, it is imperative to investigate how their quantity and quality change over time and how these factors correlate with freezing behavior in mice. Such an exploration will provide answers to this ethologically significant question raised by the reviewer. We added a paragraph in Discussion under the “The VNO as the sensor of predator cues that induce fear-related behavior” section to clarify this.

      (2) The authors claim that fresh saliva is recognized as an immediate danger by rodents, whereas old saliva is recognized as a trace of danger. However, the study lacks empirical tests to support this interpretation. With the current experimental tests, the behavioral differences between animals exposed to fresh vs. old saliva could be uniquely due to the reduced amount of the exact same protein (e.g., Fel d 4) in the two samples of saliva.

      As mentioned in response to comment 1, we agree with the alterations in both the quality and quantity of molecules within saliva after 4 hours. What we would like to emphasize in our current study is that mice detect these time-dependent changes through the VNO and subsequently adjust their defensive response patterns. Identifying the specific molecules responsible for inducing behavioral changes and investigating their time-dependent alterations is crucial in the next step. We added a paragraph in the Discussion under the 'The VNO as the sensor of predator cues that induce fear-related behavior' section to clarify this.

      (3) In Figure 4H, the authors state that there were no significant differences in the number of cFos-positive cells between the two saliva-exposed groups. However, this result disagrees with the next result section showing that fresh and old saliva differentially activate the VMH. It is unclear why cFos quantification and behavioral correlations were not performed in other upstream areas that connect the VNO to the VMH (e.g., BNST, MeA, and PMCo). That would provide a better understanding of how brain activity correlates with the different types of behaviors reported with the fresh vs. old saliva.

      We greatly appreciate this valuable advice. We added c-Fos immunoreactivity (IR) data in the BNST, MeApv, and PAG, together with the data for VMH as shown in new Figure 4G-J. Upon exposure to both fresh and old saliva, we observed an upregulation trend of cFos in the MeApv, VMH, and dPAG, but not in the BNST, compared to the control stimulus.

      Moreover, we conducted correlation analyses between the numbers of cFos-positive neurons and the duration of freezing behavior in those neural substrates, which have been added to new Figure 5. The numbers of cFos-IR signals in neurons in the BNST and dPAG did not correlate with the duration of freezing behavior in any of the exposure groups (Figure 5C, F). However, in addition to a significant positive correlation in the VMH for the fresh saliva-exposed group (R2 = 0.5708, 95% CI [-0.1449, 0.9714], p = 0.0412) (Figure 5E), we observed a similar positive correlation trend in the MeApv (R2 = 0.3854, 95% CI [0.3845, 0.9525], p = 0.0942), although it was not statistically significant possibly due to low sample numbers (Figure 5D).

      Based on these results, our current circuit model is as follows: different numbers of the VNO sensory neurons activated by fresh and old saliva result in differential excitation levels in mitral cells in the AOB. This, in turn, leads to the differential activation of targeting neural substrates, possibly MeApv, resulting in the differential activation of VMH neurons. This model is depicted in Figure 7 and discussed under the section of 'Differential processing of fresh and old saliva signals in the VNO-to-VMH pathway' in the Discussion."

      (4) The interpretation that fresh and old saliva activates different subpopulations of neurons in the VMH based on the observation that cFos positively correlates with freezing responses only with the fresh saliva lacks empirical evidence. To address this question, the authors should use two neuronal activity markers to track the response of the same population of VHM cells within the same animals during exposure to fresh vs. old saliva. Alternatively, they could use single-cell electrophysiology or imaging tools to demonstrate that cat saliva of distinct freshness activates different subpopulations of cells in the VMH. Any interpretation without a direct within-subject comparison or the use of cell-type markers would become merely speculative. Furthermore, the authors assume that differential activations of mitral cells between fresh and old saliva result in the differential activation of VMH subpopulations (page 13, line 3). However, there are intermediate structures between the mitral cells and the VMH, which are completely ignored in this study (e.g., BNST, medial amygdala).

      We appreciate this important feedback. We agree that performing a same-animal comparison for fresh and old saliva exposure will offer direct evidence of the differential activation of a sub-population of VMH neurons. However, there is technical difficulties. We have stimulated the same animal with the same or different types of swabs (e.g., Freshcontrol, fresh-fresh, fresh-old, or old-fresh) and observed that once mice were exposed to a saliva-containing swab and exhibited freezing behavior, they no longer made contact with the second swab within the timeframe when two different types of neuroactivity markers can be analyzed. As shown in Figure 2A, direct contact with the saliva swab is necessary for triggering saliva-elicited freezing behavior. Therefore, we concur that conducting further investigations into real-time neural activation responses to both fresh and old saliva within the same subjects, using an appropriate stimulus delivery method into the VNO, as demonstrated in (Bansal et al., 2021; Ben-Shaul et al., 2010; Bergan et al., 2014), would be useful to strengthen our argument.

      For the second part of the comment regarding the intermediate structures between the mitral cells and the VMH, please refer to our comment above in response to comment 3.

      (5) The authors incorrectly cited the Papes et al., 2010 article on several occasions across the manuscript. In the introduction, the authors cited the Papes et al 2010 study to make reference to the response of rodents to chemical cues, but the Papes et al. study did not use any of the chemical cues listed by the authors (e.g., fox feces, snake skin, cat fur, and cat collars). Instead, the Papes et al. 2010 article used the same chemical cue as the present study: cat saliva. The Papes et al. 2010 article was miscited again in the results section where the authors cited the study to make reference to other sources of cat odor that differ from the cat saliva such as cat fur and cat collars. Because the Papes et al. 2010 article has previously shown the involvement of Trpc2 receptors in the VNO for the detection of cat saliva and the subsequent expression of defensive behaviors by using Trpc2-KO mice, the authors should properly cite this study in the introduction and across the manuscript when making reference to their findings.

      The study conducted by Papes et al. in 2010 (Papes et al., 2010) explored mouse defensive responses triggered by native odors derived from three natural mouse predator species: cat, snake, and rat. These odors were derived from neck fur swabs, shed skin, and urine, respectively. Notably, all three types of samples induced defensive risk assessment and avoidance behaviors in mice. These responses were significantly diminished in Trpc2 knock-out (KO) mice, which lack the Trpc2 transduction channel in their vomeronasal sensory neurons, resulting in an impairment in transmitting sensory signals to the brain. Moreover, Papes et al. (2010) mentioned that, 'we did find cat saliva, a potential source of fur chemosignals, sufficient to induce c-Fos expression in the AOB and initiate defensive behavior.' While Papes et al. reported c-Fos expression in the AOB as well as behavioral responses induced by cat saliva in C57BL/6 mice, they did not provide information regarding the c-Fos expression or the defensive behavioral responses to cat saliva in Trpc2KO mice. Overall, we highly value these findings and explicitly state in the results section of our study that ‘Cat saliva has been considered as a source of predator cues found on cat fur and collars, which induce defensive behaviors in rodents (Engelke et al., 2021; Papes et al., 2010),’ providing the rationale for our utilization of cat saliva in our experimental design.

      (6) In the introduction, the authors hypothesized that the VNO detects predator cues and sends sensory signals to the VMH to trigger defensive behavioral decisions and stated that direct evidence to support this hypothesis is still missing. However, the evidence that cat saliva activates the VMH and that activity in the VMH is necessary for the expression of antipredator defensive response in rodents has been previously demonstrated in a study by Engelke et al., 2021 (PMID: 33947849), which was entirely omitted by the authors.

      We appreciate this insightful comment. Our original sentence meant that the direct evidence was missing for the hypothesis that the mouse VNO detects predator cues and sends sensory signals to the VMH, triggering appropriate defensive behavioral decisions. To clarify this, we altered the sentence (the last sentence of the second last paragraph in Introduction) to “However, how the sensory signals detected through the VNO-to-VMH circuitry modulate behavioral decisions in specific contexts remains elusive.

      The study in Engelke et al., 2021(Engelke et al., 2021) has shown that cat saliva activates the VMH and that activity in the VMH is necessary for the expression of antipredator defensive response, including freezing behavior, in rats. This important paper is now cited at multiple locations; page 4 line 16, page 9 line 8, and page 14 line 17. Interestingly, the vomeronasal receptor genes expressed in cat saliva-responsive VNO neurons, V2R-A4 subfamily genes, seem to have expanded independently within mice and rats, lacking direct V2R-A4 orthologues between mice and rats (Rocha et al. submitted). Therefore, exploring the sensory mechanism behind the induction of defensive behavioral responses in rats by cat saliva would be highly intriguing. Comparing the mechanism operating in rats with that observed in mice could offer valuable insights into understanding how the divergent sensory signaling pathways lead to the VMH-mediated defensive behavioral responses across different species.

      (7) In the discussion, the authors stated that their findings suggest that the induction of robust freezing behavior is mediated by a distinct subpopulation of VMH neurons. The authors should cite the study by Kennedy et al., 2020 (PMID: 32939094) that shows the involvement of VMH in the regulation of persistent internal states of fear, which may provide an alternative explanation for why distinct concentrations of saliva could result in different behavioral outcomes.

      We appreciate this valuable advice to cite this important paper. It is now cited at page 14 line 17 in the Discussion under “Differential activation of VMH neurons potentially underlying distinct intensities of freezing behavior.” We agree that it is intriguing to hypothesize that different freshness of cat saliva induces different degree of persistence of neural activity in a subpopulation of VMH neurons, which regulates the freezing behavior intensity.

      (8) The anatomical connectivity between the olfactory system and the ventromedial hypothalamus (VMH) in the abstract is unclear. The authors should clarify that the VMH does not receive direct inputs from the vomeronasal organ (VNO) nor the accessory olfactory bulb (AOB) as it seems in the current text.

      We apologize for the confusion caused by our statement in the abstract. The reviewer is correct that the VMH does not receive direct inputs from the VNO and AOB. The abstract now states: 'The vomeronasal organ (VNO) is one of the major sensory input channels through which predator cues are detected with ascending inputs to the medial hypothalamic nuclei, especially to the ventromedial hypothalamus (VMH), through the medial amygdala (MeA) and bed nucleus of the stria terminalis (BNST).’

      Reviewer #2 (Public Review):

      Weakness:

      The findings are relatively preliminary. The identities of the receptor and the ligand in the cat saliva that induces the behavior remain unclear. The identity of VMH cells that are activated by the cat saliva remains unclear. There is a lack of targeted functional manipulation to demonstrate the role of V2R-A4 or VMH cells in the behavioral response to cat saliva.

      We concur with the reviewer’s comments and agree with the necessity to explore the behavioral response to cat saliva in mice with V2R-A4 receptor(s) knocked out, alongside those with targeted functional manipulations in the VMH. These future studies will allow us to further elucidate the molecular and neural mechanisms underlying this sensory-tohypothalamic circuit.

      Reviewer #3 (Public Review):

      Weaknesses:

      (1) It is unclear if fresh and old saliva indeed alter the perceived imminence predation, as claimed by the authors. Prior work indicates that lower imminence induces anxiety-related actions, such as re-organization of meal patterns and avoidance of open spaces, while slightly higher imminence produces freezing. Here, the authors show that fresh and old predator saliva only provoke different amounts of freezing, rather than changing the topography of defensive behaviors, as explained above. Another prediction of predatory imminence theory would be that lower imminence induced by old saliva should produce stronger cortical activation, while fresh saliva would activate the amygdala, if these stimuli indeed correspond to significantly different levels of predation imminence.

      We thank the reviewer for this valuable insight. In our current study, we exclusively compared defensive behavioral responses to 15-minute-old and 4-hour-old cat saliva in mice within their home cages. In future studies, it would be intriguing to expand this investigation by examining behavioral changes in response to saliva collected at additional time points across diverse behavioral settings. Additionally, exploring neural activity in various brain regions in future studies would complement our understanding of these responses.

      (2) It is known that predator odors activate and require AOB, VNO, and VMH, thus replications of these findings are not novel, decreasing the impact of this work.

      We acknowledge the previous findings mentioned by the reviewer. Our finding in this paper is that cat saliva samples with different freshness predominantly activate different numbers of VNO sensory neurons expressing the same subfamily of sensory receptors, which results in differential activation of the downstream circuit to modulate behavioral outputs.

      (3) There is a lack of standard circuit dissection methods, such as characterizing the behavioral effects of increasing and decreasing the neural activity of relevant cell bodies and axonal projections, significantly decreasing the mechanistic insights generated by this work.

      We thank the reviewer for the valuable comments. We acknowledge that exploring the behavioral effects through the manipulation of specific cell types within defined neural substrates, along with characterizing circuit connectivity, is crucial to understand this circuit more thoroughly in future studies.

      (4) The correlation shown in Figure 5c may be spurious. It appears that the correlation is primarily driven by a single point (the green square point near the bottom left corner). All correlations should be calculated using Spearman correlation, which is non-parametric and less likely to show a large correlation due to a small number of outliers. Regardless of the correlation method used, there are too few points in Figure 5c to establish a reliable correlation. Please add more points to 5c.

      We thank the reviewer for this important suggestion. We assessed normality of the data using the Shapiro-Wilk and Kolmogorov-Smirnov tests, confirming that the dataset is parametric. We anticipate employing a larger sample size in future studies to further examine rigorous correlation patterns.

      (5) Some of the findings are disconnected from the story. For example, the authors show that V2R-A4-expressing cells are activated by predator odors. Are these cells more likely to be connected to the rest of the predatory defense circuit than other VNO cells?

      Yes, our hypothesis posits that V2R-A4-expressing VNO sensory neurons serve as receptor neurons for predator cues present in cat saliva. Additionally, we assume that these specific sensory neurons have stronger anatomical connections with the defensive circuit compared to VNO sensory neurons expressing other receptor subfamilies. In our modified Discussion section, we discussed this point under “V2R-A4 subfamily as the receptor for predator cues in cat saliva.”

      (6) Were there other behavioral differences induced by fresh compared to old saliva? Do they provoke differences in stretch-attend risk evaluation postures, number of approaches, the average distance to odor stimulus, the velocity of movements towards and away from the odor stimulus, etc?

      We appreciate the reviewer's valuable comments. We have now incorporated an analysis of stretch-sniff risk assessment behavior, presented in new Figure 1F (graph) and Supplemental Figure 1B (raster plot). Mice exhibited stretch-sniff risk assessment behavior, which remained consistent across control, fresh saliva, and old saliva swabs. Additionally, we have also included a raster plot for direct investigation, previously noted as ‘interaction’ in the original manuscript (Supplemental Figure 1C). Mice exposed to a swab containing either fresh or old saliva significantly avoided directly investigating the swab. In contrast, mice exposed to a clean control swab spent a significant amount of time directly investigating the swab, engaging in behaviors such as sniffing and chewing (Figure 1G). A comparison of temporal behavioral patterns revealed a slightly higher frequency of direct investigation behavior toward old saliva compared to fresh saliva at the beginning of the exposure period (Supplemental Figure 1C).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (A) In the discussion (page 13, line 13), the authors proposed approaches to isolate receptors among the V2R-A4 subfamily that could be responsible for the detection of predator cues in cat saliva such as mRNA profiling from cells isolated from VNO GCaMP imaging. However, the authors argue that this method can lead to false positive results. The authors should clarify what they mean by this exactly.

      We meant that pairing of kairomones and their cognate vomeronasal receptors is overall challenging, and subsequent confirmations by performing loss-of-function, as well as gainof-function studies, are necessary to avoid false positive receptor-ligand pairings. We modified the sentence in the discussion as follows: “…. as well as receptor mRNA profiling from isolated single cells activated by cat saliva in GcaMP imaging using the VNO slices in vitro (Haga-Yamanaka et al., 2014; Wong et al., 2020). Receptor candidates identified using either of the methods can be further confirmed by examining necessity and sufficiency for detecting cat saliva using genetically modified mouse lines.”

      (B) In the discussion, the authors mention that imminent predator cues present in the cat saliva activate a specific population of VMN neurons. However, the authors have not demonstrated that imminent predator cues exist and the differences between fresh and old saliva are not simply a matter of concentration and integrity of the same protein (see a similar concern in item 2 above).

      In alignment with our responses to the reviewer’s public comments 1 and 2, we acknowledge the changes in both the quality and quantity of molecules in cat saliva when kept at room temperature for 4 hours. Our findings demonstrate that mice detect this timedependent alteration through the VNO, leading to subsequent adjustments in their defensive response patterns. The identification of specific molecules responsible for inducing behavioral changes and an exploration of their time-dependent alterations are crucial steps in our ongoing research. To provide further clarification, we have added a paragraph in the discussion section under 'The VNO as the sensor of predator cues that induce fear-related behavior.’

      (C) In the introduction, the authors cite several studies and reviews that investigated sensory neural circuits that mediate behavioral responses to chemical predator cues in mice. However, the majority of these studies used rats. Therefore, it is recommended to instead indicate that these studies focus on using rodent models.

      We appreciate this insightful comment. We have now replaced the term 'mice/mouse' with 'rodents' in corresponding parts of the manuscript.

      (D)The description of the extended amygdala is unclear and gives the impression that the posteroventral part of the medial amygdala is also part of the extended amygdala (page 3, line 25).

      We appreciate the reviewer’s important feedback. We have removed the phrase 'the extended amygdala consisting of' from the text.

      (E) The authors should justify why they have focused on the role of V2R-A4 in cat saliva detection. As shown in the Figure 3A schematic, many other receptors within the V2R family could have been evaluated. Additionally, the authors should indicate how many mice were used for calculating the ratio for each receptor in Figure 3C, and a group comparison should be performed.

      As shown in Supplemental Figure 2 and Figure 3C, our initial investigation involved assessing the co-localization of pS6 signals with signals derived from in situ hybridization probes for all V2R subfamilies. Each probe was designed to recognize all the receptor genes within the subfamily under the tested conditions. This examination led to the identification of V2R-A4, whose probe signals overlap with pS6 signals induced by exposure to cat saliva. In Figure 3C, the percentage of total overlap between the in situ probe and pS6 signals in VNO sections was examined from n=3-6 animals, which is now mentioned in the modified figure legend.

      (F) The authors should make it clear to readers at the very beginning of the manuscript that the behavioral differences between fresh and old saliva are not caused by the inefficiency of the old cat saliva to induce defensive responses. Thus, other antipredator behavioral responses should be also quantified (e.g., avoidance time, number and time of investigations to the cat saliva source, risk-assessment, etc.)

      We appreciate this valuable comment from the reviewer. In the original version of our manuscript, we used the term 'interaction' to indicate 'direct interaction with the swab for investigation.' We have now replaced the term 'interaction' with 'direct investigation' and added the temporal patterns of these behavioral episodes in Supplemental Figure 1C. Our observations indicate that mice avoid directly investigating both fresh and old saliva compared to the control (Figure 1G). However, there is a slight increase in investigation behavior toward old saliva at the beginning of exposure compared to fresh saliva (Supplemental Figure 1C). Furthermore, we have included the duration (Figure 1F) and temporal patterns (Supplemental Figure 1B) of stretch-sniff risk assessment behavior. Notably, stretch-sniff behavior did not differ towards control, fresh, and old saliva swabs.

      (G) The selected representative images for Gαo- and pS6-labeled neurons in Figure 2 should have similar levels of DAPI labeling. Further, the plot depicting the duration of freezing as a function of pS6-IR signals in the VNO (Figure 2H) is difficult to follow. The authors should indicate on the graph which data points represent fresh or old cat saliva exposure, similar to the style used in Figure 5 plots.

      We have replaced the representative image in Figure 2E to align the DAPI intensity. Additionally, we updated the data points in Figure 2H and introduced a color code to indicate saliva types.

      (H) The schematic in Figure 4 is misleading because the AOB does not directly project to the VMH. The authors should explain which regions are conveying indirect predator information from AOB to VMH (see a similar concern in item 7 above).

      We thank the reviewer’s important feedback. We modified the image in Figure 4A to show the entire defensive behavior circuit initiated from the VNO.

      Reviewer #2 (Recommendations For The Authors):

      (1) This result suggests that V2R-A4 may be the dominant VR for mice to detect cat saliva.

      Future studies should determine the identity of the receptor and the ligand in the cat saliva. Additionally, the functional importance of V2R-A4 remains unclear. It is important to knockout the receptor and test changes in cat saliva-induced freezing.

      We concur with the reviewer’s comments and recognize the necessity of exploring the behavioral response to cat saliva in mice with V2R-A4 receptor(s) knocked out. Moreover, the identification of the ligand in cat saliva is critical for a deeper understanding of the molecular mechanisms in future studies.

      (2) AOB does not project to VMH directly. Other known important nodes for the predator defense circuit include MeApv, BNST, PMd, AHN, and PAG. It will be helpful to provide c-Fos data in those regions (especially MEA and BNST as they are between AOB and VMH) to provide a complete picture of how the brain processes cat saliva to induce the behavior change.

      We appreciate this important feedback by the reviewer. We have now added c-Fos expression analysis data in the BNST, MeApv, and PAG, in addition to the VMH. Upon exposure to fresh and old saliva, we observed the upregulation of cFos in the MeApv, VMH, and dPAG, but not in the BNST, compared to the control stimulus. The data are now shown in Figure 4G-J. Moreover, we also added correlation analyses between the numbers of cFospositive neurons and the duration of freezing behavior in those neural substrates to Figure 5. The numbers of cFos-IR signals in neurons in the BNST and dPAG, did not correlate with the duration of freezing behavior in any of the exposure groups (Figure 5C, F). However, in addition to a significant positive correlation in the fresh saliva-exposed group in the VMH (R2 = 0.5708, 95% CI [-0.1449, 0.9714], p = 0.0412) (Figure 5E), we observed a similar positive correlation trend in the MeApv (R2 = 0.3854, 95% CI [-0.3845, 0.9525], p = 0.0942), although it was not statistically significant possibly due to low sample numbers (Figure 5D). Based on these results, our current circuit model is as follows: different numbers of the VNO sensory neurons activated by fresh and old saliva result in differential excitation levels in mitral cells in the AOB. Differential excitation of mitral cells leads to the differential activation of targeting neural substrates, possibly MeApv, which results in differential activation of VMH neurons. This model is depicted in Figure 7 and discussed under the section of “Differential processing of fresh and old saliva signals in the VNO-toVMH pathway” in Discussion.

      (3) It is interesting that activation level difference in the VNO by old and fresh cat saliva does not transfer to AOB. It could be informative to examine the correlation between VNO and AOB p6/c-Fos cell number and AOB and VMH c-Fos cell number across animals to understand whether the activation levels across those regions are related. If they are not correlated, it could be helpful to add a discussion regarding potential reasons, e.g. neuromodulatory inputs to the AOB.

      We agree that analyzing the number of pS6/cFos-positive cells from all the regions in the same animals are ideal; however, due to technical difficulties, we were unable to collect the entire set of neural substrates from the same animals.

      (4) Please indicate n in all figure plots and specify what individual dots mean. In Figure 4h, there are 7 dots in the old saliva group, presumably indicating 7 animals. In Figure 6b, there appear to be more than 7 dots for the old cat saliva group. Are there more than 7 animals? If so, why are they not included in Figure 4h? If not, what does each dot mean? Note that each dot should represent an independent sample. One animal should not contribute more than one dot.

      We apologize for the confusion about Figure 6b. Each of these dots indicates the number of cFos signals in a single VMH hemisphere sample. The data used for this analysis were the same as the ones for the VMH used in Figure 4. This is now clarified in the figure legends.

      (5) The identification of a cluster of VMHdm cells uniquely activated by fresh cat saliva urine is interesting. It will be important to identify the molecular handle of the cells to facilitate further investigation. This could be achieved using either activity-dependent RNAseq or double in situ of saliva-induced c-Fos and candidate genes (candidate gene may be identified based on the known gene expression pattern).

      We agree that these experiments are very valuable. We would like to perform those experiments in future studies.

      Reviewer #3 (Recommendations For The Authors):

      (1) Please cite recent relevant papers showing VMH activity induced by predators, such as https://pubmed.ncbi.nlm.nih.gov/33115925/ and https://pubmed.ncbi.nlm.nih.gov/36788059/

      We thank the reviewer’s suggestion to cite these important papers. https://pubmed.ncbi.nlm.nih.gov/33115925/ (Esteban Masferrer et al., 2020) and https://pubmed.ncbi.nlm.nih.gov/36788059/ (Tobias et al., 2023) are now cited at page 14 line 17 in the Discussion under “Differential activation of VMH neurons potentially underlying distinct intensities of freezing behavior.”

      (2) Add complete statistical information in the figure legends of all figures, which should include n, name of test used, and exact p values.

      We included statistical analysis results in figure legends; for Figure 6B, we provided statistical analysis results in Supplemental Table 1.

      (3) Please paste all figure legends directly below their corresponding figure to make the manuscript easier to read.

      We have added figure legends directly below their corresponding figures.

      Editor's note:

      Should you choose to revise your manuscript, please include full statistical reporting including exact p-values wherever possible alongside the summary statistics (test statistic and df) and 95% confidence intervals. These should be reported for all key questions and not only when the p-value is less than 0.05.

      Statistics analysis results have been included in figure legends and supplemental table 1.

      References

      Bansal R, Nagel M, Stopkova R, Sofer Y, Kimchi T, Stopka P, Spehr M, Ben-Shaul Y. 2021. Do all mice smell the same? Chemosensory cues from inbred and wild mouse strains elicit stereotypic sensory representations in the accessory olfactory bulb. BMC Biol 19:133.

      Ben-Shaul Y, Katz LC, Mooney R, Dulac C. 2010. In vivo vomeronasal stimulation reveals sensory encoding of conspeciic and allospeciic cues by the mouse accessory olfactory bulb. Proc Natl Acad Sci U S A 107:5172‒5177.

      Bergan JF, Ben-Shaul Y, Dulac C. 2014. Sex-speciic processing of social cues in the medial amygdala. Elife 3:e02743.

      Engelke DS, Zhang XO, OʼMalley JJ, Fernandez-Leon JA, Li S, Kirouac GJ, Beierlein M, Do-Monte FH. 2021. A hypothalamic-thalamostriatal circuit that controls approachavoidance conlict in rats. Nat Commun 12:2517.

      Esteban Masferrer M, Silva BA, Nomoto K, Lima SQ, Gross CT. 2020. Differential Encoding of Predator Fear in the Ventromedial Hypothalamus and Periaqueductal Grey. J Neurosci 40:9283‒9292.

      Papes F, Logan DW, Stowers L. 2010. The vomeronasal organ mediates interspecies defensive behaviors through detection of protein pheromone homologs. Cell 141:692‒703.

      Tobias BC, Schuette PJ, Maesta-Pereira S, Torossian A, Wang W, Sethi E, Adhikari A. 2023. Characterization of ventromedial hypothalamus activity during exposure to innate and conditioned threats. Eur J Neurosci 57:1053‒1067.

    1. o the death of a whale proves meaningful to a vibrant hostof dependent creatures, even as it may look senseless from the shore

      It is important that these whales die in the sea because their bodies can be food for deep-sea animals for hundreds of years, supplying the ecosystem. I agree with the author that is a beautiful and natural process that is so sad it is being disrupted by humans.

    Annotators

    1. Author Response

      eLife assessment

      This study, which seeks to identify factors from the glial niche that support and maintain neural stem cells, unveils a novel role for ferritin in this process. Furthermore, the work shows that defects in larval brain development resulting from ferritin knockdown can be attributed to impaired Fe-S cluster activity and ATP production. These findings will be valuable to both oncologists and neurobiologists, though the supporting evidence is currently incomplete.

      Public Reviews

      Reviewer #1 (Public Review):

      Summary:

      This study unveils a novel role for ferritin in Drosophila larval brain development. Furthermore, it pinpoints that the observed defects in larval brain development resulting from ferritin knockdown are attributed to impaired Fe-S cluster activity and ATP production. In addition, knocking down ferritin genes suppressed the formation of brain tumors induced by brat or numb RNAi in Drosophila larval brains. Similarly, iron deficiency suppressed glioma in the mice model. Overall, this is a well-conducted and novel study.

      Strengths:

      Thorough analyses with the elucidation of molecular mechanisms.

      Weaknesses:

      Some of the conclusions are not well supported by the results presented.

      We really appreciate your review and positive feedback. As for weaknesses, we will try our best to solidate the related conclusions.

      Reviewer #2 (Public Review):

      Summary:

      Zhixin and collaborators have investigated if the molecular pathways present in glia play a role in the proliferation, maintenance, and differentiation of Neural Stem Cells. In this case, Drosophila Neuroblasts are used as models. The authors find that neuronal iron metabolism modulated by glial ferritin is an essential element for Neuroblast proliferation and differentiation. They show that loss of glial ferritin is sufficient to impact on the number of neuroblasts. Remarkably, the authors have identified that ferritin produced in the glia is secreted to be used as an iron source by the neurons. Therefore iron defects in glia have serious consequences in neuroblasts and likely vice versa. Interestingly, preventing iron absorption in the intestine is sufficient to reduce NB number. Furthermore, they have identified Zip13 as another regulator of the process. The evidence presented strongly indicates that loss of neuroblasts is due to premature differentiation rather than cell death.

      Strengths:

      • Comprenhensive analysis of the impact of glial iron metabolism in neuroblast behaviour by genetic and drug-based approaches as well as using a second model (mouse) for some validations.

      • Using cutting-edge methods such as RNAseq as well as very elegant and clean approaches such as RNAi-resistant lines or temperature-sensitive tools

      • Goes beyond the state of the art highlighting iron as a key element in neuroblast formation as well as as a target in tumor treatments.

      Weaknesses:

      Although the manuscripts have clear strengths, there are also some strong weaknesses that need to be addressed.

      • Some literature is missing

      Thanks for your reminder and we will add the missing literatures.

      • In general, the authors succeeded but in some cases, the authors´ claims are not fully supported by the evidence presented and additional experiments are critical to discriminate among different hypotheses.

      We are greatly grateful to the reviewer for recognizing our work, and we will support our conclusions with further evidence.

      • Moreover, some potential flaws might be present in the analysis of cell death and mitochondrial iron.

      We used Caspase-3 or TUNEL to indicate the apoptosis signal. Further, we overexpressed the anti-apoptosis gene p35 to inhibit apoptosis and found no rescue effect on neuroblast number. The results of these experiments are consistent.

      It is difficult to determine the mitochondrial iron of neuroblast, so we used indirect methods to test ferroptosis, such as TEM and iron (or iron chelator) supplement. We will perform more experiments according to recommendations to determine that.

      Reviewer #3 (Public Review):

      In this manuscript, Ma et al seek to identify stem cell niche factors. They perform an RNAi screen in glial cells and screen for candidates that support and maintain neuroblasts (NBs) in the developing fly brain. Through this, they identify two subunits of ferritin, which is a conserved protein that can store iron in cells in a non-toxic form and release it in a controlled manner when and where required. They present data to support the conclusion that ferritin produced in glia is released and taken up by NBs where it is utilised by enzymes in the Krebs cycle as well as in the electron transport chain. In its absence from glia, NBs are unable to generate sufficient energy for division and therefore prematurely differentiate via nuclear prospero resulting in small brains. The work will be of interest to those interested in neural stem cells and their non-cell autonomous control by niches.

      The past decade has seen a growing appreciation of how glial cells support and maintain NBs during development.

      The authors' discovery of glial-derived ferritin providing essential iron atoms for energy production is interesting and important. They have employed a variety of genetic tools and assays to uncover how ferritin in glia might support NBs. This is particularly challenging because there are no direct ways of assaying for iron or energy consumption in a cell-specific manner.

      There are however instances where conclusions are drawn to support the story being developed without considering the equally plausible alternative explanations that should ideally be addressed.

      For example, the data supporting the transfer of ferritin from glia to NBs was weak given the misexpression system used; the Shi[ts] experiment was also not convincing (perhaps they have more representative images?).

      Thanks for your comment. We have the negative control, which excludes the misexpression. As for Shits experiment, we will substitute for more representative images.

      The iron manipulation experiments are in the whole animal and it is likely that this affects general feeding behaviour, which is known to affect NB exit from quiescence and proliferative capacity. The loss of ferritin in the gut and iron chelators enhancing the NB phenotype are used as evidence that glia provide iron to NB to support their number and proliferation. Since the loss of NB is a phenotype that could result from many possible underlying causes (including low nutrition), this specific conclusion is one of many possibilities.

      Iron chelator (or iron salt) feeding is a common method for investigating metal metabolism in Drosophila[1-3]. And other metal chelators (such as copper and zinc chelator) do not have similar phenotype (data not shown), which can partially exclude this possibility. Further, iron absorption was blocked by knockdown of ferritin only in the iron cell region[1], a small part of midgut, which phenocopied iron chelator feeding, implying iron deficiency is probably the main cause of the phenotype. More importantly, iron chelator only enhances the NB phenotype in the ferritin knockdown group, not the control group, suggesting iron deficiency results in the phenotype, which rules out other possibilities.

      Similarly, knockdown of the FeS protein assembly components phenocopy glial ferritin knock down. Since iron is so important for the TCA and the ETC, this is not surprising, but the similarities in the two phenotypes seem insufficient to say that it's glial ferritin that's causing the lack of iron in the NB and therefore resulting in loss of NBs.

      It is hard to get this conclusion just by FeS protein assembly components knockdown, so we just used “implied” to describe this result. However, we combine several results to address this issue, including iron chelator feeding, ferritin knockdown in the midgut, the enhancement of phenotype by iron chelators, aconitase activity, GO enrichment, KEGG enrichment, and Zip13. These results pointed to the interpretation that iron deficiency in NBs caused by glial ferritin defects leads to NB loss.

      Pros RNAi will certainly result in an increase in NB numbers because the loss of pros results in an inability of NB progeny to differentiate. This (despite the slight increase in nuclear pros) is not sufficient to infer that glial ferritin knockdown results in premature differentiation of NBs via nuclear pros.

      First, pros RNAi, brat RNAi, or numb RNAi can each result in an inability of NB progeny to differentiate, respectively[4-6]. If the rescue of NB number by pros RNAi mainly relies on the differentiation block of NB progeny, brat RNAi or numb RNAi is expected to similarly rescue the NB number. However, our results showed that only pros RNAi could rescue the NB number, while brat RNAi or numb RNAi could not.

      Secondly, nuclear Pros represses genes required for self-renewal and is also required to activate genes for terminal differentiation[7]. Thus, Pros is kept in the cytoplasm and remains almost undetectable in the nuclei in normal NBs[8]. However, we observed the detectable Pros in the nuclei of some NBs after glial ferritin knockdown, and the NB number with detectable nuclear Pros was significantly increased when compared to control.

      Altogether, we conclude that NBs tend to undergo premature differentiation after glial ferritin knockdown.

      I recognise these are challenging to prove irrefutably, however, the frequency of such expansive interpretations of data is of concern.

      (1) Tang X, Zhou B. Ferritin is the key to dietary iron absorption and tissue iron detoxification in Drosophila melanogaster. FASEB J, 2013,27(1):288-98

      (2) Xiao G, Liu ZH, Zhao M, et al. Transferrin 1 Functions in Iron Trafficking and Genetically Interacts with Ferritin in Drosophila melanogaster. Cell Rep, 2019,26(3):748-58 e5

      (3) Mukherjee C, Kling T, Russo B, et al. Oligodendrocytes Provide Antioxidant Defense Function for Neurons by Secreting Ferritin Heavy Chain. Cell Metab, 2020,32(2):259-72 e10

      (4) Knoblich JA, Jan LY, Jan YN. Asymmetric Segregation of Numb and Prospero during Cell-Division. Nature, 1995,377(6550):624-7

      (5) Zacharioudaki E, Magadi SS, Delidakis C. bHLH-O proteins are crucial for neuroblast self-renewal and mediate Notch-induced overproliferation. Development, 2012,139(7):1258-69

      (6) Bello B, Reichert H, Hirth F. The brain tumor gene negatively regulates neural progenitor cell proliferation in the larval central brain of. Development, 2006,133(14):2639-48

      (7) Choksi SP, Southall TD, Bossing T, et al. Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neural stem cells. Developmental Cell, 2006,11(6):775-89

      (8) Spana EP, Doe CQ. The Prospero Transcription Factor Is Asymmetrically Localized to the Cell Cortex during Neuroblast Mitosis in Drosophila. Development, 1995,121(10):3187-95

    1. Reviewer #2 (Public Review):

      Summary:<br /> The authors describe the discovery of a filovirus neutralizing antibody, AF03, by phage display, and its subsequent improvements to include NPC2 that resulted in greater breadth of neutralization. Overall, the manuscript is much improved from first review.

      While the authors only use docking studies and this does not convincingly map the AF03 epitope, they do provide compelling evidence that residues Q128, N129, and possibly C226 are part of the epitope or at least close enough to affect binding and neutralisation. This is not conclusive support for their assumption that AF03 targets the NPC1 binding site. However, the authors do show that AF03 competes for MR78 binding to its epitope (in the NPC1 binding site), and this is enough to roughly place the epitope in this region (barring the possibility of an adjacent binding site with steric occlusion of the MR78 epitope).<br /> The authors provide evidence for broad neutralisation, and also provide good support for the internalization of AF03-NL as the mechanism for improved breadth over the original AF03 antibody.

      Strengths:<br /> This study shows convincing binding to Marburgvirus GP and neutralization of Marburg viruses by AF03, as well as convincing neutralization of Ebolaviruses by AF03-NL. While there is not good separation of PE-stained populations by FACS in figure 5A, the cell staining data in Figure 5C are compelling to a non-expert in endosomal staining like myself. The control experiments in Figure 7 are compelling showing neutralization by AF03-NL but not AF03 or NPC2 alone or in combination. Altogether these data support the internalisation and stabilisation mechanism that is proposed for the gain in neutralization breadth observed for Ebolaviruses by AF03-NL over AF03 alone.

      Weaknesses:<br /> To support their affinity measurements, the authors argue that they show GP is a monomer in Figure 1A by SDS-PAGE. SDS-PAGE cannot be used to assess oligomerisation of GP. Native PAGE or size exclusion profiles would have been better suited to this purpose. If affinity was calculated on a 1GP:2IgG binding sites as the authors imply, then the affinity data are incorrect due to avidity effects. As suggested by a previous reviewer, using monomeric Fab would solve this problem.

      The information for figure 2 states: "we investigated if this mutated MARV species was STILL sensitive o AF-03 treatment". But, "we sought to determine whether AF-03 could impede pseudotyped MARV viral entry" only happens in Figure 3. This information for figure 3 has now already been determined in Figure 2 where wildtype MARV is neutralised (black curves) introducing redundancy. The authors should first show that AF-03 can neutralise MARV pseudotyped virus, and then assess whether mutants are STILL sensitive to AF-03.

      Figure 1: The visualisation of AF03 modelling and docking is better on a white background, but still difficult to interpret as currently presented. The labels of predicted contact residues are still impossible to read, and the yellow text does not show. As suggested previously, a zoom-in showing predicted co-location with Q128 and N129 would show these data better. It would also be useful to orient the reader with respect to trimeric membrane bound GP.

      Figure 2: The presentation of these data is much improved and support the text.

      Figure 3: The presentation of these data is much improved and support the text.

      Figure 4: The presentation of these data is much improved and support the text.

      Figure 5: The presentation of these data is much improved and support the text.

    1. Reviewer #1 (Public Review):

      In this study, the authors investigate the role of triglycerides in spermatogenesis. This work is based on their previous study (PMID: 31961851) on triglyceride sex differences in which they showed that somatic testicular cells play a role in whole body triglyceride homeostasis. In the current study, they show that lipid droplets (LDs) are significantly higher in the stem and progenitor cell (pre-meiotic) zone of the adult testis than in the meiotic spermatocyte stages. The distribution of LDs anti-correlates with the expression of the triglyceride lipase Brummer (Bmm), which has higher expression in spermatocytes than early germline stages. Analysis of a bmm mutant (bmm[1]) - a P-element insertion that is likely a hypomorphic - and its revertant (bmm[rev]) as a control shows that bmm acts autonomously in the germline to regulate LDs. In particular, the number of LDs is significantly higher in spermatocytes from bmm[1] mutants than from bmm[rev] controls. Testes from males with global loss of bmm (bmm[1]) are shorter than controls and have fewer differentiated spermatids. The zone of bam expression, typically close to the niche/hub in WT, is now many cell diameters away from the hub in bmm[1] mutants. There is an increase in the number of GSCs in bmm[1] homozygotes, but this phenotype is probably due to the enlarged hub. However, clonal analyses of GSCs lacking bmm indicate that a greater percentage of the GSC pool is composed of bmm[1]-mutant clones than of bmm[rev]-clones. This suggests that loss of bmm could impart a competitive advantage to GSCs, but this is not explored in greater detail. Despite the increase in number of GSCs that are bmm[1]-mutant clones, there is a significant reduction in the number of bmm[1]-mutant spermatocyte and post-meiotic clones. This suggests that fewer bmm[1]-mutant germ cells differentiate than controls. To gain insights into triglyceride homeostasis in the absence of bmm, they perform mass spec-based lipidomic profiling. Analyses of these data support their model that triglycerides are the class of lipid most affected by loss of bmm, supporting their model that excess triglycerides are the cause of spermatogenetic defects in bmm[1]. Consistent with their model, a double mutant of bmm[1] and a diacylglycerol O-acyltransferase 1 called midway (mdy) reverts the bmm-mutant germline phenotypes.

      There are numerous strengths of this paper. First, the authors report rigorous measurements and statistical analyses throughout the study. Second, the authors utilize robust genetic analyses with loss-of-function mutants and lineage-specific knockdown. Third, they demonstrate the appropriate use of controls and markers. Fourth, they show rigorous lipidomic profiling. Lastly, their conclusions are appropriate for the results. In other words, they don't over-state the results. Overall, the rigorously quantified results support the major aim that appropriate regulation of triglycerides are needed in a germline cell-autonomous manner for spermatogenesis.

      This paper should have a positive impact on the field. First and foremost, there is limited knowledge about the role of lipid metabolism in spermatogenesis. The lipidomic data will be useful to researchers in the field who study various lipid species. Going forward, it will be very interesting to determine what triglycerides regulate in germline biology. In other words, what functions/pathways/processes in germ cells are negatively impacted by elevated triglycerides. And as the authors point out in the discussion, it will be important to determine what regulates bmm expression such that bmm is higher in later stages of germline differentiation.

  4. Feb 2024
    1. Reasons for Using E-Tivities

      De facto a questão de conhecermos as razões para o uso de e-atividades torna-se pertinente nos atuais contextos de aprendizagem, no sentido em que, esta pode ser facilitada pelo uso de e-atividades, contribuindo para o grau de envolvimento e de motivação dos formandos. Isto é, a aprendizagem é mais efetiva quando o tema em estudo é significativo para o formando; uma vez perante um tema do seu interesse, o formando consegue aprender mais e melhor. A aprendizagem é mais fácil quando se gosta do tema/assunto em que se está a estudar. Ora, é neste ponto em que as e-atividades podem influenciar positivamente este processo uma vez que, podem tornar mais interativo e, logo, mais interessante qualquer tema que, à partida pudesse ser menos interessante para o formando, dando-lhe assim a oportunidade de aprofundar conhecimentos num tema que provavelmente não seria da sua iniciativa e daí a oportunidade de alargar o seu horizonte em termos de conhecimento. Por outro lado, sabemos também que a aprendizagem consegue ser mais bem sucedida quando envolve uma “ação” e por isso, o uso de e-atividades em muito pode contribuir para que o tema em estudo seja assimilado de forma mais célere e efetiva, dado que, o investimento de um esforço próprio na realização da e-atividade tornará os conteúdos mais significativos para o formando.

    2. Abstract

      Sumariamente, o estudo destaca a importância do design eficaz de aprendizagem online, explorando o método E-tivities como uma possível abordagem para atender os componentes da Comunidade de Investigação (CoI). Os resultados sugerem que os E-tivities têm potencial para abordar todas as Presenças da CoI, com ênfase na Expressão Afetiva para a Presença Social e na organização inicial do curso para a Presença de Ensino.

    3. All of the participants had their own specific individual and personal challenge in designing E-tivities, with only two participants over-lapping on one particular challenge.

      Este aspeto sugere os seguintes fatores, ou uma combinação deles: - Os participantes adotaram metodologias de desenho diferenciadas com caraterísticas e dificuldades próprias. - Diferentes áreas de ensino apresentam desafios diferenciados. - O volume/qualidade/tipo de e-tividades produzidas pelos vários participantes não é comparável. - Os recursos (tempo/tecnologia/orçamento...) disponíveis para cada participante são diversos. - A experiência e competência de cada um dos participantes na criação destes recursos é variável.

      A grande variabilidade de resultados torna o valor "científico" destes resultados menos interessante do que outros disponibilizados neste mesmo artigo.

      Jorge Barreiros, 2305097 - Docência Digital em Rede (2ª Edição) 2023 04

    4. Research into online learning suggests the most reported area for dissatisfaction/satisfaction in the online learning environment was the quality of the encouragement, feedback, counselling, facilitation, respect and instructional quality of the teacher [35,36,37,38,39].

      Diria que as qualidades aqui enunciadas são fundamentais para qualquer professor, seja em regime presencial ou "à distância". O ambiente digital tanto pode ser um veículo para a sua transmissão, como um obstáculo à manifestação destas qualidades.Em função desta referência, inclino-me para afirmar que o segundo cenário será mais provável. Por exemplo, é sabido que a ausência da componente não verbal na comunicação escrita dificulta a transmissão e perceção de estado de espírito e intenção, o que leva a que seja, naturalmente, mais difícil fomentar a empatia entre professor e aluno (ou, porque não, entre alunos no paradigma de ensino em rede).

      Jorge Barreiros - MC: Docência Digital em Rede (2ª Edição) 2023 04

    5. Obviously there are limitations of this research from many different avenues, including issues in generalisability outside of this particular case study approach and the small sample size.

      Tendo em consideração a metodologia seguida no trabalho, os resultados referem o volume de discussão de determinados aspetos, o que não é, necessariamente, diretamente correspondente com a sua importância ou relevância (um assunto pode ser discutido por ser, por exemplo, mais controverso ou complexo - tal não reflete necessariamente a sua importância).

      Jorge Barreiros - 2305097

    6. Research into online learning suggests the most reported area for dissatisfaction/satisfaction in the online learning environment was the quality of the encouragement, feedback, counselling, facilitation, respect and instructional quality of the teacher [35,36,37,38,39]. In other words, their “teaching presence”. It is not innovative to suggest the role of the teacher in learning is a pivotal one, and yet online students still continue to be dissatisfied with their experience and their engagement with their teachers. Some research [40,41] suggests that the reason for this is because teachers are often not adequately confident or literate in online teaching skills or pedagogy, and that those with less exposure to online learning have less positive views of its implementation [42].

      O papel do professor na aprendizagem online é fundamental e exige habilidades. Um dos principais desafios da aprendizagem online, é a falta de interação entre professor e aluno. Sendo por isso importante criar estratégias para promover a comunicação e o feedback entre professor e aluno. O uso de ferramentas tecnológicas adequadas pode facilitar a interação e o acompanhamento dos alunos. É necessário investir na formação e desenvolvimento dos professores para o ensino online para melhorar a experiência e o envolvimento dos alunos. Tânia Rodrigues

    7. many educators cite difficulties in adapting their current traditional teaching methods to these theoretically complex approaches

      Por isso, ser importante existir este tipo de formação, para nos dar a conhecer novas ferramentas e tudo o que envolve uma comunidade virtual de aprendizagem interativa, colaborativa e investigativa.

      Carla Oliveira, estudante 2305044, Fev 24

    8. A par do videoAnt reconheço também o potencial desta ferramenta no suporte à aprendizagem digital. Como desafios à docência presente e num futuro próximo, destaco da leitura do artigo a necessidade de i) capacitar o corpo docente para a utilização destas ferramentas - que os sucessivos confinamentos vieram tornar mais evidente, mas também ii) a adaptação das IES, quer ao nível do desenho de novas ofertas formativas, à disponibilização de formação pedagógica do corpo docente, e no seu reflexo na avaliação de desempenho.

    9. Blogs offer substantial benefits for social scientific

      Concordo, eu própria já usei a informação de publicação em websites e blogs para analisar o clima emocional vivido no Euro 2004 (antes, durante e depois do acontecimento) e a informação obtida provém de um contexto natural que nos permite recolher muitos dados.

      Cristina Sousa Fev 2024

    10. Estando as atividades de aprendizagem digital associadas às diferentes ações que os estudantes realizam em interação com o sistema online, os conteúdos e a comunidade virtual de aprendizagem, retenho a importância dos alunos como atores centrais na criação do conhecimento de forma colaborativa, ativa e participativa. Motivadoras, envolventes e intencionais, devem ser moderadas por um professor (e-moderador, com os objetivos de socializar o grupo, moderar a partilha de ideias, facilitar o acesso à informação e ao conhecimento e auxiliar no processo de pesquisa e desenvolvimento do pensamento crítico). Parece-me que, embora orientadas por objetivos bem definidos, podem apresentar alguns fragilidades na sua avaliação adequada. Considero curioso que a área mais relatada de insatisfação/ satisfação no ambiente de aprendizagem on-line se relacionasse com a qualidade do incentivo, feedback, aconselhamento, facilitação, respeito e qualidade instrucional do professor, sentindo na minha prática diária este mesmo constrangimento: falta de confiança ou alfabetização em habilidades de ensino on-line.

    11. Um aspeto que me parece central é perceber-se que estudantes temos nos dias de hoje. Não podemos esquecer que, na sua maioria, são nativos digitais, habituados desde sempre a "mexer" em dispositivos tecnológicos. Contudo, isso não faz deles proficientes na separação do lixo que circula pelas redes daquilo que verdadeiramente é conhecimento. Por outro lado, a sua "ubiquidade" tecnológica em que estão permanentemente em "não lugares" conduz a uma forma diferente de aprendizagem que as instituições educativas têm de saber usar. Não basta usar sistemas tradicionais e complementá-los com e-atividades pretensamente motivadoras. Há que repensar todo o processo de educação. Carlos Afonso Uaberta 2/2024 2305021

    12. his study utilised a qualitative method approach, which is an approach that is more interpretive and descriptive analysis of data [19,20] over quantitative and empirical methods (with a

      Excelente o progresso registado até à data no caminho da educação e aprendizagem virtual. No entanto, quando a diversidade de documentos e ferramentas de apoio é exagerada tal gera o caos. A perplexidade que um ambiente virtual traz ao tempo que é designado para atingir objectivos específicos de aprendizagem exige que o "caminho" deve estar muito bem definido pelos orientadores ou docentes.

    13. Social Presence;Cognitive Presence; andTeaching Presence.

      Três dimensões a valorizar necessariamente numa e-atividade. Sem a presença de todos os elementos humanos do ecossistema digital (professor e alunos), o potencial da e-atividade ficará muito limitado.

    14. . The most important component for adequate Teaching Presence factors was the initial Design and Organisation

      A seleção, conceção e organização da e-Atividade é sem dúvida uma das condicionantes do sucesso do processo de aprendizagem. Sem uma escolha adequada dos recursos a usar corre-se o risco de que os objetivos não sejam alcançados. Por outro lado se a e-atividade não estiver bem estruturada, corremos o risco de não conseguir o interesse, motivação e empenho dos alunos.

    15. y ensuring that their teachers actually know how to teach, rather than simply being experts in the field that they teach

      Infelizmente em algumas IES a qualidade de ensino não é o principal objetivo…

    16. participate in professional development training

      Isto sim é essencial. É urgente que os dirigentes das IES entendam isto… este documento tem 10anos, e muita coisa não mudou… Adicionalmente, na minha área que é engenharia, a grande maioria dos docentes não tem qualquer formação em pedagogia, vão dar aulas, muitas vezes mimetizando os seus professores… O que é referido é de extrema importância, deveria ser obrigatório a quem ingressa na carreira docente, ter algum tipo de formação na área das ciências da educação.

    17. disappointment

      Como já referi várias vezes, este é um problema que não é exclusivo do online. Naturalmente, como disse o colega, numa sala de aula virtual, a porta da saída está a um clique… ou então se for algo síncrono, é desligar a câmara e já está… a distrações são muitas (redes sociais, Telemovel, etc), mas é aqui que temos de ver isto como uma oportunidade… o ambiente de aprendizagem tem de ser criado de forma a aumentar o “engagement” do estudante… e ter a noção do tempo que ele consegue manter a concentração… todas as fases de uma e-atividade têm de ter isto em consideração, e pode haver fases que permitam o estudante descontrair, para depois voltar ao trabalho…

    18. ffer diverse activities

      Garantir que se conhece o público-alvo e que todos se sentem incluídos é essencial para garantir que todos têm a oportunidade de atingir os objetivos estabelecidos ao seu ritmo.

    19. benefits

      É interessante que o beneficio da redução do abandono escolar seja de apenas 6%… provavelmente por serem realidades diferentes do nosso pais, e por este é um artigo com 10 anos. Efetivamente, no que se refere à minha experiência, a taxa de abandono escolar tem vindo cada vez a aumentar mais… a distância social e física dos nossos estudantes, que frequentam cursos presenciais (logo um mindset diferente de alguém quite ingressa num curso online), o aumento do absentismo às aulas, muitas vezes porque consideram essas aulas aborrecidas e as substituem por videos do youtube, aliadas à sua falta de método de estudo, torna estas e-atividades de uma importância significativa para os trazer de novo à presença do professor, nem que seja através de ambientes virtuais. Esta é sem dúvida, no meu POV, a forma de contribuirmos para o sucesso dos estudantes e para termos diplomadas com elevada competência científica.

    20. Blog data

      Este sim tem sido um aumento exponencial… No entanto, há alturas é que são tantas e sobre tantas coisas, e muitas vezes o “blogger” nem é especialista no assunto… como garantir que os estudantes não utilizam estas fontes de informação como verdades absolutas… vivemos no mundo dos bloggers, influencers, YouTubers, e mais uns quantos **ers… esta abertura para o mundo digital e a sua utilização (que eu própria faço) não poderá levar os alunos a considerarem estas fontes como fidedignas?

    21. online

      É efetivamente necessário mudar a visão e as estratégias de ensino, porque o perfil dos nossos estudantes está a mudar… e essa é a minha principal motivação para realizar estas formações. Neste sentido, coloco a seguinte questão, eu aplico novas metodologias porque acredito que são a forma de contribuirmos para o sucesso dos nossos estudantes, mas todas estas mudanças requerem motivação e tempo, e quando somos os “únicos”, será que conseguimos atingir o objetivo pretendido? Estas novas metodologias dão mais trabalho ao docente, e na grande maioria das vezes também ao estudante… se formos o único a fazer, não irá o estudante encarar como sendo o “tal” professor que nos faz trabalhar demais??

    22. Challenges for Designing E-Tivities

      Apesar da clareza na definição prévia dos objetivos de aprendizagem, para mim, a avaliação das e-atividades apresenta-se, de facto, com um dos maiores desafios, principalmente quando asseguramos, sozinhos, várias unidades curriculares com um número significativo de alunos (+/- 70). Estimular a motivação dos alunos para que se mantenham focados e interessados nas e-atividades é, na minha perspectiva, outro desafio que considero não ser totalmente ultrapassado com o garantir que o conteúdo da e-atividade seja relevante e interessante e com o recurso a vários elementos interativos que podem aumentar o envolvimento dos alunos e até facilitar a aprendizagem. Se o aluno não é suficientemente autónomo e autodisciplinado, mantê-lo ativo e presente cognitivamente é um desafio.

      Paula Godinho

    23. strategies in e-Moderation

      Fazer uma e-moderação pode parecer uma tarefa simples, porém, por experiência própria, sei que só é possível com uma formação/capacitação adequada. Quando ministrava aulas em uma escola de ensino secundário, tinha acesso à diversos recursos online (ferramentas e plataformas). Porém, não tive qualquer formação a não ser 1h de capacitação em como utilizar o quadro digital. Nessa aula nos foram apresentadas as ferramentas, porém só apresentadas. Aprender a utilizá-las leva tempo e prática, o que nem sempre é possível, fazendo com que, às vezes, as e-atividades e as e-moderações fiquem apenas na esfera do moodle e de softwares simples.

      Estou gostando muito de ter contato com essas "ferramentas" que estamos utilizando no curso, tanto do hypothes.is como o Video Ant me supreenderam muito positivamente e com certeza as utilizarei, seja em cursos online, à distância ou presenciais.

    24. E-tivities are utilised weekly and consistently through course modules, are recommended to be deployed in groups of 25 people maximum

      Há quem ouse propor e-atividades em unidades curriculares frequentadas por mais de 250 alunos... A estratégia é propor semanalmente mais do que uma e-Atividade e os alunos responderão às e-Atividades que lhes sejam mais favoráveis, desafiantes ou apelativas. Esta semana apresentei um Objeto de Ensino e Aprendizagem (OEA) nas aulas presenciais sobre o Polinómio de Taylor, dediquei 2 horas ao assunto (aula presencial) e no final apresentei-lhes a "e-Atividade: Polinómio de Taylor" para desenvolverem uma aplicação mais completa e robusta que a apresentada... Arménio Correia turma 4

    25. training online educators in the strategies E-tivities, e-Moderation, and the 5-Stage Model

      A capacitação dos professores para e-atividades e a e-moderação é fundamental para a adequação destes à era digital que estamos presenciando. Esta é necessária não apenas para a familiarização com as ferramentas, tecnologias e plataformas, no sentido de implementar as atividades de maneira competente, mas para promover o engajamento dos alunos, uma vez que atividades online podem ser muito envolventes, quando bem planeadas e executadas. Embora não seja uma regra, muitas vezes, os alunos utilizam muito mais ferramentas e tecnologias do que os professores. Mas, como já evidenciado pela literatura, essa utilização pode não ser eficiente, principalmente quando estão relacionadas com as atividades de ensino e aprendizagem. Nesse sentido, é importante que os professores sejam capacitados tanto para a utilização quando para a motivação do uso pelos alunos e, para isso, é necessário “estar presente”, participar das discussões, levantar questões, propor desafios e tudo mais.

    26. designing E-tivities, with only two participants over-lapping on one particular challenge

      O design de e-atividades alinhadas com o Salmon Stage Model permite criar e-atividades mais estruturadas e com melhor qualidade segundo os peritos, cujos blogs foram analisados neste artigo. Dois dos peritos consideram que “as etapas 1 e 2 são cruciais para garantir que as outras etapas funcionem”, ou seja o acesso e motivação e a socialização, duas etapas que me parecem muito desafiantes no design das e-atividades. As e-atividades associadas a e-moderação e ao modelo de 5 etapas permitem a implementação de uma estrutura de design de aprendizagem alinhada com os fatores sociais, de ensino e de presença cognitiva da estrutura CoI, no âmbito da pedagogia construtivista.

    27. “Focus on learning, not technology”, and were appropriate to the overarching category “Benefits of E-tivities”.

      O princípio de que o conhecimento é construído pelo aluno de forma participativa e colaborativa reforça não só os benefícios como a importância das e-atividades serem concebidas e desenvolvidas de forma a motivar os alunos (Salmon, 2002) promovendo o desenvolvimento de competências e habilidades que potenciem a autonomia e a responsabilidade dos mesmos no seu próprio processo de aprendizagem.

      As e-atividades podem tornar a experiência de aprendizagem mais enriquecedora, personalizada e envolvente se atendermos ao facto de que para além de facilitarem e estimularem as aprendizagens colaborativas, também permitem um maior respeito pelo ritmo do aluno na exploração e realização da atividade.

      Paula Godinho

    28. E-tivities

      Ferramentas como o VideoAnt e o Hypotes.is contribuem para a implementação de e-atividades diferentes e motivadoras. Pessoalmente acho o VideoAnt mais inovador e interessante para usar, na medida em que existem ferramentas colaborativas que já usamos e em que já é possível adicionar comentários, mas o uso de diferentes ferramentas permite criar e-atividades diferentes e que vão ao encontro de diferentes estilos de aprendizagem dos alunos.

    29. The 5-Stage Model

      Na parte final do vídeo de apresentação desta semana 3 de formação, o Professor António Moreira refere que “Nas salas de aula virtuais deve-se socializar o grupo, moderar a partilha de ideias, facilitar o acesso à informação e ao conhecimento e auxiliar no processo de pesquisa e desenvolvimento do pensamento crítico”. O modelo das 5 fases baseado nas pesquisas de Salmon [Salmon, G. E-Moderating: The Key to Teaching and Learning Online, 3rd ed.; Routledge/Falmer: New York, NY, USA, 2011] assenta num conjunto de etapas que de algum modo me parece que espelham estas características ou preocupações referidas pelo Professor António Moreira.

    30. They must also negate the complexities surrounding the current disruptive and unstable climates of online education and institutional economic security

      Sem prejuízo de todas as vantagens inerentes ao desenho das E-atividades segundo o 5-Stage Model, nomeadamente com a contemplação dos quatro componentes da Presença Cognitiva, torna-se essencial que o desenho de uma E-atividade bem estruturada possa colmatar algumas limitações/constrangimentos. Uma delas aqui identificada, é a pressão para se fazerem convergir as atuais ideologias e práticas de ensino, com as ferramentas e expectativas do ensino digital em rápida expansão, o que levado ao extremo no ensino das artes e do trabalho prático realizado em ciências, poderá simultaneamente traduzir-se numa redução de orçamento destinado à compra de materiais para construção de obras e/ou modelos analógicos, também muito relevantes no desenvolvimento de competências estruturantes. Assim uma reflexão interessante que poderá ser realizada é “Será que estamos a integrar adequadamente as E-atividades com as atividades analógicas, promovendo um ensino híbrido de boa qualidade?” Noutra situação, com o intuito de se promover uma E-atividade colaborativa, onde os estudantes participem ativamente de forma envolvente e intencional, tal como descrita pelo Professor António Moreira, é verdadeiramente necessário que se possa ultrapassar os climas disruptivos instáveis que por vezes se instalam na educação on-line, desprovendo-a de um propósito bem claro e baixando os níveis de motivação dos participantes. Desta forma, a mediação/orientação dos professores assume um papel fulcral, não só na escolha das plataformas e softwares digitais que se irão utilizar no desenvolvimento das diferentes aprendizagens e competências, mas também na gestão do ambiente que se estabelece entre os participantes, com o objetivo último de criar uma verdadeira comunidade de aprendizagem.

    31. Specifically, as they become familiar with the structure over time, it allows them to not get caught up in the distractions of design and technology, and focus directly on the task at hand.

      Algo bastante importante. O design e a tecnologia devem ser algo de motivador, mas não podem ser um meio de distração e de distanciamento do papel principal das e-atividades: realização das tarefas a que se propõem.

      Francisco Miranda

      UAb: Docência Digital em Rede, 02/2024

      N.º Estudante: 2305062

    32. Research into online learning suggests the most reported area for dissatisfaction/satisfaction in the online learning environment was the quality of the encouragement, feedback, counselling, facilitation, respect and instructional quality of the teacher

      Também considero serem aspetos fundamentais...pela experiência já tida como estudante e, também, como professora num curso em formato blended learning. A identificação de ambientes virtuais e e-atividades em que o estudante saiba o quê, como, quando e para quê, para além de que também se sinta estimulado a participar e a partilhar dúvidas, a possa ter feedbacks rápidos face às suas dúvidas, são elementos que considero fundamentais para garantir a motivação e o interesse pelo processo de aprendizagem.

      Sandra Saúde Nº de estudante: 2305083

    33. O "5 Stage Model" de Gilly Salmon baseia-se numa estrutura de aprendizagem gradual, que facilita o envolvimento dos alunos. O incentivo dado à interação colaborativa é uma mais valia. É um modelo flexível, centrado no aluno, adaptável a a diversos contextos educativos. A presença em todas as fases do e-moderanting promovendo uma aprendizagem autônoma mas com suporte constante.

    34. (see http://www.gillysalmon.com/1/category/guest%20blogger/1.html).

      Recomendo a navegação até à webpage de Gilly Salmon, onde a autora apresenta e disponibiliza vários recursos (texto, vídeo, infogramas) interessantes relacionados com as e-atividades e com, o "5 Stage Model" Pedro Moreira, n.º 2305074, 2023 03

    35. Blogs offer substantial benefits for social scientific research providing similar, but far more extensive opportunities than their “offline” parallel of qualitative diary research. First, they provide a publicly available, low-cost and instantaneous technique for collecting substantial amounts of data. Further, blogs are naturalistic data in textual form, allowing for the creation of immediate text without the resource intensiveness of tape recorders and transcription (p. 92).

      Interessante esta visão dos blogs! Esta não é uma tecnologia digital interessante para utilizarmos? A aprendizagem e os sentimentos emocionais são facilmente transmitidos de uma forma instantânea. Efetivamente, penso que é uma ferramenta importante para o ensino-aprendizagem.

      Francisco Miranda

      UAb: Docência Digital em Rede, 02/2024

      N.º Estudante: 2305062

    36. As e-atividades devem ser concebidas e desenvolvidas de forma a garantir a motivação do estudante e, ao mesmo tempo, serem orientadas para a prossecução de objetivos. Devem ter como função a estimulação das aprendizagens profundas e do aprender a aprender, devem ainda promover a transferência de conhecimentos entre diferentes contextos e a sua aplicação a contextos profissionais, onde os estudantes se venham a inserir. As e-atividades podem ser concebidas de forma assíncrona ou de forma síncrona. As e-atividades de qualidade devem promover um papel ativo do estudante, estimulando uma aprendizagem autónoma, ajudando-o a elaborar o seu próprio conhecimento, a partir da interação com outras pessoas e/ou recursos digitais. Devem, ainda, levar os mesmos a refletir, de forma metacognitiva, sobre o desenvolvimento e os resultados do trabalho realizado, procurando promover a aplicação ou a transferência de processos cognitivos para novos cenários e contextos.

      Rita Teixeira d'Azevedo (nº 2305041) - MC: Docência Digital em Rede (2ª Edição) 2023 02

    37. By ensuring that their teachers actually know how to teach, rather than simply being experts in the field that they teach. For one of the key principles in successful knowledge construction within students is how well their educators deliver that knowledge, effectively and inspirationally.

      Para a prática docente de um professor, a intencionalidade é fundamental, pois dela se alimentam todas as escolhas e desenho do processo de ensino-aprendizagem que pretende promover, nas dimensões cognitiva, social e afetiva. Só assim as suas propostas podem ser "inspiradoras" do conhecimento em construção e das competências em desenvolvimento nos discentes. Aliás, em grande medida só a perceção destes poderá dar efetiva informação ao docente sobre a qualidade da sua proposta, uma e-atividade ou uma sequência didática. Aqui se joga a "liberdade de aprender e de ensinar", um dos direitos, liberdades e garantias que a nossa Constituição consagra (https://www.parlamento.pt/Legislacao/Paginas/ConstituicaoRepublicaPortuguesa.aspx#art43)). As opções pedagógicas individuais ou de pequeno grupo deverão desejavelmente alinhar-se com as estratégias institucionais que as enquadram. Sabemos que este é um problema significativo em muitas instituições. Não se conseguem desenhar boas atividades de aprendizagem em ambientes digitais em rede de forma consistente e continuada, sem o apoio de meios técnicos, nomeadamente humanos. Meios tecnológicos em opensource são um recurso sempre provisório, pela ausência de contratual com a instituição onde trabalhamos. No que aos conteúdos diz respeito, valha-nos o Acesso Aberto, pela disponibilização de literatura científica e académica. Cum grano salis o devemos considerar, por não estar imune às estratégias predatórias de tantas revistas ou a fenómenos de cartelização de citações. Maria do Sameiro Masseno - IPBeja - 23.02.2024

    38. It could be concluded by this research that there is some potential support for an alignment between the CoI framework being operationalised through the use of E-tivities [6], e-Moderation [17] and the 5-Stage Model [6].

      Não obstante as limitações que este estudo poderá ter, e que foram apontadas/(a)notadas por diversos Colegas ao longo do artigo, julgo que ele aborda de forma interessante os múltiplos desafios que se colocam ao Professor /Formador na eficaz operacionalização das várias dimensões/fatores presentes na conceção, desenvolvimento e gestão de contextos de aprendizagem digital em rede assentes nos modelos de community of inquiry (CoI), e na articulação/interação com os conceitos/processos de e-tivities, e-moderation e 5-stage model que temos vindo a estudar no âmbito deste módulo. O estudo traz para o centro da reflexão/do debate o conceito e a importância das e-tividades na conceção/desenho/desenvolvimento do modelo pedagógico (virtual). Os resultados do estudo reforçam a importância da adequada conceção/seleção de e-tividades para atingir cada um dos objetivos específicos das várias fases/vertentes do processo de aprendizagem em contexto virtual e em rede. Maria João Ramos

    1. eLife assessment

      This valuable study provides the detailed molecular mechanism of how OGT, an O-GlcNac transferase, promotes cancer progression. Using loss-of-function OGT models, the authors demonstrated that OGT cleaves HCF-1, a guardian of genomic stability. These solid findings can lead to some potential approaches to modulate anti-tumor immunity by targeting this process.

    2. Reviewer #1 (Public Review):

      Summary:

      This study provides the detailed molecular mechanism of how OGT, an O-GlcNac transferase, promotes cancer progression. Using loss-of-function OGT models, the authors demonstrated that OGT cleaves HCF-1, an important guardian of genomic stability. The resulting genomic instability in OGT-knockout tumors leads to cytosolic DNA accumulation, the activation of cGAS-mediated type I IFN responses, and increased CD8+ T cell infiltration into the tumors. Moreover, treatment with OGT inhibitor synergized with anti-PDL1 immune-checkpoint blockade.

      Strengths:

      Novel findings of how OGT promotes tumor progression.

      Weaknesses:

      (1) Some of the data is problematic and does not always support the authors' conclusions.<br /> (2) The writing needs significant improvement. In places, it is hard to understand or could mislead the readers.<br /> (3) Figure legends are minimalistic and do not provide sufficient information.<br /> (4) Discussion does not put the findings of this study into a broader context of the field but merely restates them.

    3. Reviewer #2 (Public Review):

      Summary:

      In this study, the author demonstrates that deficiency or pharmacological inhibition of O-glcNac transferase (OGT) enhances tumor immunity in colorectal cancer models. The authors propose that OGT deficiency triggers a DNA damage response, activating the cGAS-STING innate immunity pathway and promoting a Type I interferon response. They suggest that OGT-mediated processing of HSF1 is crucial in maintaining genomic integrity. This research is significant as it identifies OGT inhibition as a potential immunomodulatory target in cancer treatment.

      Strengths:

      The strength of the paper lies primarily in the in vivo data, demonstrating the impact of OGT deficiency or inhibition on modulating tumor growth and anti-tumor immunity. The experiments are well-controlled. However, there are several unresolved questions:

      Weaknesses:

      The mechanisms of how OGT deficiency can trigger DNA damage and the role of this response in promoting immunity are only partially addressed in the manuscript.

    1. Якщо ніхто не може уникнути цієї взаємозалежності, тоді ми всі рівні, але в іншому сенсі. Всі ми рівнозалежні

      Так, всі ми взаємозалежні, але я б не стала однозначно стверджувати про те, що ми рівнозалежні і в цьому як раз проблема. Так білі жінки виключають чорних, чоловіки жінок, феміністки транс людей, адже по відношенню до них вони є домінуючою групою.

    2. З іншого боку, деякі з тих, хто підписав цей лист, критикували Black Lives Matter, ніби гучний і публічний опір расизму – сама по собі некультурна поведінка. Деякі протестували проти громадянських прав для Палестини. Інші [за деякими твердженнями] чинили сексуальне насильство. Були серед них і ті, хто не сприймає критики за свій расизм.

      Мені здається так буде завжди - кожна велика група чи категорія може включат и індивідів з дуже різними категоріями. Але це не скасовує певних емержентних властивостей.

    3. «відчинити двері туалетів і роздягальень для будь-якого чоловіка, який вважає або відчуває себе жінкою» і тим самим, можливо, наразити жінок на ризик насильства.

      На мою думку, на проблему жіночих та чоловічих туалетів слід дивитись інакше. А саме, замість того, аби задавати питання, що робити з тими чоловіками поставити питання про доцільність розділення туалетів за статтю, і чи є взагалі у цьому сенс. Чомусь в кожній квартирі у нас немає двох окремих туалетних кімнат. Звісно, цьому можна протиставити те, що жінки у загальному просторі можуть не почувати себе у безпеці серед чоловіків з багатьох причин. Однак це не означає, що потрібно обмежувати права транс людей, замість того, щоб на суспільному рівні вирішувати проблему сексуалізованого насилля, тощо.

    4. Что вы можете сказать о языке ненависти и насилия, который используется онлайн против таких людей, как Дж. К. Роулинг

      я постійно помічаю, що дане питання найчастіше піднімають щодо супер відомих, заможних та привілейованих людей. знову ж таки, люди, що не мають даних речей потребують таких питань і загалом допомоги набагато більше, однак цього не відбувається, адже в них немає голосу.

    5. позиция Трампа, заявившего, что гендер должен определяться биологическим полом, и попытки протестантизма и правого католицизма зачистить образование и публичную политику от «гендера»

      це завжди так цікаво для мене, адже при цьому гендерні стереотипи, мізогінія і сексизм зберігаються, фемінність і маскулінність розрізняються і соціальні очікування залишаються, але слово гендер викликає в них проблеми

    6. Я думаю, що ми живемо в антиінтелектуальні часи і це відбивається на всіх секторах політичного спектру. Швидкість соціальних мереж уможливлює такі ступеня жовчності, які зовсім не сприяють вдумливій дискусії. Потрібно цінувати та підтримувати повільні форми.

      Мені дуже відгукується теза про підтримку повільних форм, дійсно соціальні мережі часто уможливлюють шалений потік ненависті та інших форм гноблення людьми одне одного, але також погоджуюся з коментарем Алєсі, що без соцмереж ми не мали б такої можливості висловлювати свої погляди та сприймати різноманітність поглядів інших людей.

    7. Когда тебя десятилетиями не слышат, крик о справедливости неизбежно будет гром

      дуже влучна фраза. Стосується будь-яких груп і течій. Її б варто було усвідомити противникам прайдів як "пропаганди".

    8. антиинтеллектуальные времена

      я з цим згодна, але водночас коли ми жили в добу інтелектуальних елітарних суспільств, то жінки були замкнені в золотих клітках, а дискусія про гендери взагалі не була можливою. Зараз ми маємо майданчик для висловлення й можемо легше знаходити спільноту собі подібних, щоб виразити себе.

    9. Мы передаем исторические знания о том, что означало быть женщиной в ту или иную эпоху, в том или ином месте, и видим, как эти категории со временем менялись.

      я справді мало знаю про транслюдей і хотіла б дізнатися як вони вирішують для себе питання гендеру. Тобто так в 19, 20 сторіччі є чітка модель що таке чоловік і що таке жінка , між ними можна обрати. Наразі кордони поведінки й самовираження більш гнучкі, тож можна бути фемінним_ою чи маскулінним_ою без прив'язки до статі. В такому разі в чому суть саме гендерного переходу вважати себе жінкою чи чоловіком? (ну це більше мої роздуми в повітря)

    10. Такая позиция предполагает, что пенис – это и есть угроза и что любой человек с пенисом, определяющий себя как женщину, устраивает подлый, лживый и вредный маскарад.

      мені здається це не зовсім коректним в дискусії. Батлер роздуває аргумент, доводить його до максимуму. Я не вважаю (думаю Роулінг також), що кожна людина з членом небезпечна й намагається проникнути в жіночу роздягальню саме з ціллю згвалтувати, однак я не можу виключати можливості, що хтось таки цього бажає і може скористатися лазівкою. Аналогія з дитячим садком: загалом люди не помишляють робити щось з дітьми, але є педофіли, тому територія дитячих садків закрита й входити можуть тільки ті, хто забирає дітей у вихователів.

      Я не знаю який вихід. Можливо створення окремої роздягальні для трансгендерних людей? але й це множення варіацій також не є продуктивним.

    1. Gabor and his team developed a model for the light-harvesting systems of plants and applied it to the solar spectrum measured below a canopy of leaves. Their work made it clear why what works for nanotube solar cells doesn’t work for plants: It might be highly efficient to specialize in collecting just the peak energy in green light, but that would be detrimental for plants because, when the sunlight flickered, the noise from the input signal would fluctuate too wildly for the complex to regulate the energy flow.

      Ciertamente, si se produjeran variaciones intermitentes en la llegada de luz solar a la atmósfera a corto plazo, como por ejemplo alteraciones climáticas o un aumento en las expulsiones de masa coronal, podrían generar un exceso o déficit de electrones en las plantas. En consecuencia, se presentarían fallos al no contar con la energía necesaria para llevar a cabo sus funciones vitales, o la planta tendría que buscar una manera de liberar el exceso de energía. En ambos casos, es probable que la planta experimentara un desenlace fatal.

  5. 3ad5c237-7dcf-4014-b052-345b96b6dcf6.filesusr.com 3ad5c237-7dcf-4014-b052-345b96b6dcf6.filesusr.com
    1. Capítulo 1. Importancia de la medición y el error

      Me parece muy importante tener presentes este tipo de tablas, porque muchas veces al resolver o estar leyendo acerca de estos se nos puede ir el hilo, por esta razón es muy importante

    1. Understanding the nuance of multicultural practices is critically important, given the current struggle to teach about culture and difference. Although this study highlights the experiences of students and teachers at one urban high school, examining their experiences in-depth allows us to understand how difference plays o

      I completely agree with the importance of understanding the nuance of multicultural practices, but I think something important to consider that aids this fight is how diverse schools have become. There are more diverse friend groups which help aid in the fight to learn more about the cultures of others and the hardships they face.

  6. inst-fs-iad-prod.inscloudgate.net inst-fs-iad-prod.inscloudgate.net
    1. e don't need multicultural education here; most of our students are White." "I don't see color. All my students are the same to me." "We shouldn't talk about racism in school because it has nothing to do with learning. Besides, it'll just make the kids feel bad." "Let's not focus on negative things. Can't we all just get along?" In discussing multicultural education with teachers and other educators ovker h h . ·1 remar s. many years, we ave eard all these comments and other s1m1 ar I S h h f lticultura tatements sue as t ese reflect a profound misconception o mu education. . . . k f lessons When multicultural education is mentioned, many people first thin ° . 11 • h l . ducauo m uman re a hons and sensitivity training, units about ethnic holidays, e

      This is an extremely toxic perspective on the topic, especially the portion speaking about how most of the students are white. I strongly believe that White people are the exact group that needs to understand and learn the importance of multicultural education. Because they are the group who have typically chosen to be ignorant to people of color.

    1. Résumé de la vidéo [00:00:10][^1^][1] - [00:25:19][^2^][2]:

      Cette vidéo présente un débat sur les structures fondamentales des sociétés humaines, animé par un sociologue qui discute de divers sujets, notamment la sociologie de l'éducation, la création littéraire, l'individu dans la société, et la sociologie des rêves.

      Points forts: + [00:00:10][^3^][3] Introduction du débat * Présentation du sociologue + [00:00:45][^4^][4] Sociologie de l'éducation * Importance de l'éducation dans la structure sociale + [00:01:01][^5^][5] Création littéraire * Influence de Kafka et la théorie du champ + [00:01:23][^6^][6] Rôle de l'individu * L'individu façonné et façonnant le monde social + [00:01:44][^7^][7] Sociologie des rêves * Exploration de l'inconscient socialement structuré + [00:02:04][^8^][8] Engagement public du sociologue * Réponse à des critiques sociales actuelles + [00:04:14][^9^][9] Scientificité des sciences sociales * Discussion sur l'épistémologie et la méthodologie + [00:07:50][^10^][10] Différences entre sciences sociales et sciences dures * Débat sur la relativité et la cumulativité des connaissances + [00:08:57][^11^][11] Lois en sciences sociales * Tentatives et défis de formuler des lois sociales + [00:13:08][^12^][12] Objet changeant des sciences sociales * Comparaison avec les sciences expérimentales et historiques + [00:16:29][^13^][13] Expérimentation en sciences sociales * Limites et possibilités d'expérimentation avec des groupes humains + [00:20:07][^14^][14] Sciences sociales comme sciences historiques * Défi de formuler des lois pour une réalité en constante évolution + [00:23:03][^15^][15] Cumulativité en sciences sociales * Nécessité d'accumuler et de formaliser les connaissances Résumé de la vidéo [00:25:22][^1^][1] - [00:50:36][^2^][2]:

      La vidéo aborde les structures fondamentales des sociétés humaines, en débattant des idées reçues sur les sciences sociales par rapport aux sciences naturelles. Elle souligne l'importance de la comparaison intersociétés et interespèces pour comprendre les sociétés humaines et leurs invariants, comme les dimensions économiques et magico-religieuses présentes dans toutes les sociétés.

      Points clés: + [00:25:22][^3^][3] Darwin et l'évolution * Remise en question de la fixité des espèces * Introduction de la notion de transformation et d'évolution + [00:27:47][^4^][4] Complexité des objets d'étude * Rejet de l'idée que les sciences sociales étudient des objets plus complexes * Comparaison avec la diversité des planètes et des espèces + [00:30:17][^5^][5] Prédiction en sciences * Discussion sur la capacité de prédiction des sciences sociales et physiques * Importance du contexte et des détails pour la prédiction + [00:34:46][^6^][6] Structures fondamentales des sociétés * Identification de lignes de force invariantes dans toutes les sociétés humaines * Exemples de dimensions économiques et magico-religieuses + [00:37:49][^7^][7] Comparaison et évolution * Nécessité de comparaisons intersociétés et interespèces pour l'analyse sociale * Influence des propriétés biologiques sur l'organisation sociale Résumé de la vidéo [00:50:38][^1^][1] - [01:02:23][^2^][2]: La vidéo discute des structures fondamentales des sociétés humaines, en se concentrant sur l'altricialité secondaire chez les humains et ses implications sociales et culturelles.

      Points forts: + [00:50:38][^3^][3] Altricialité secondaire * Dépendance longue et forte chez les humains * Nécessité d'apprendre et de socialisation + [00:52:45][^4^][4] Maturité sexuelle tardive * Risque évolutif et protection des enfants * Coopération pour la survie de l'espèce + [00:54:11][^5^][5] Éducation collective * Importance de la communauté dans l'éducation * Coopération et dépendance sociale + [00:56:18][^6^][6] Dominance et structures sociales * Présence de la domination dans toutes les sociétés * Influence de la biologie sur l'organisation sociale + [00:57:15][^7^][7] Géronocraties et hiérarchie sociale * Domination des aînés sur les jeunes * Impact de la longévité sur la culture et la mémoire sociale

    1. Fusing standard and popular urban and rural varieties, calé sprinkles in a handful of terms borrowed from the argot of Mexico and other Hispanic areas,

      Aprender tanto sobre la fusión de lenguaje me hace pensar en la comida, o sea en la fusión de ingredientes y culturas diferentes para crear distintos platos ...

    2. her language, particularly when the source language belongs toa politically or economically dominant group.

      ¡Nunca he pensado en cómo los préstamos ocurren cuando el idioma fuente pertenece de un grupo dominante políticamente o económicamente!

    3. The type of contact is also very important as it determines those areas or domains where language shifting or borrowing is likely to occur.

      En lo tocante a los origines de los préstamos, hay que notar que son resultados del intercambio entre grupos diferentes. Algunos ejemplos incluyen la ocupación o coexistencia de grupos extranjeros en una tierra, las guerras, o cualquier fenómeno en que hay contacto íntimo entre hablantes de varios idiomas.

    1. o people can enslave another for centuries without coming out with a notion of super- iority, and when the color and other physical traits of those peoples were quite different it was inevitable that the prejudice should take a racist form.

      **

    1. Reviewer #1 (Public Review):

      The authors deploy a combination of their own previously developed computational methods and databases (SIGNOR and CellNOptR) to model the FLT3 signaling landscape in AML and identify synergistic drug combinations that may overcome the resistance AML cells harboring ITD mutations in the TKI domain of FLT3 to FLT3 inhibitors. I did not closely evaluate the details of these computational models since they are outside of my area of expertise and have been previously published. The manuscript has significant issues with data interpretation and clarity, as detailed below, which, in my view, call into question the main conclusions of the paper.

      The authors train the model by including perturbation data where TKI-resistant and TKI-sensitive cells are treated with various inhibitors and the activity (i.e. phosphorylation levels) of the key downstream nodes are evaluated. Specifically, in the Results section (p. 6) they state "TKIs sensitive and resistant cells were subjected to 16 experimental conditions, including TNFa and IGF1 stimulation, the presence or absence of the FLT3 inhibitor, midostaurin, and in combination with six small-molecule inhibitors targeting crucial kinases in our PKN (p38, JNK, PI3K, mTOR, MEK1/2 and GSK3)". I would appreciate more details on which specific inhibitors and concentrations were used for this experiment. More importantly, I was very puzzled by the fact that this training dataset appears to contain, among other conditions, the combination of midostaurin with JNK inhibition, i.e. the very combination of drugs that the authors later present as being predicted by their model to have a synergistic effect. Unless my interpretation of this is incorrect, it appears to be a "self-fulfilling prophecy", i.e. an inappropriate use of the same data in training and verification/test datasets.

      My most significant criticism is that the proof-of-principle experiment evaluating the combination effects of midostaurin and SP600125 in FLT3-ITD-TKD cell line model does not appear to show any synergism, in my view. The authors' interpretation of the data is that the addition of SP600125 to midostaurin rescues midostaurin resistance and results in increased apoptosis and decreased viability of the midostaurin-resistant cells. Indeed, they write on p.9: "Strikingly, the combined treatment of JNK inhibitor (SP600125) and midostaurin (PKC412) significantly increased the percentage of FLT3ITD-TKD cells in apoptosis (Fig. 4D). Consistently, in these experimental conditions, we observed a significant reduction of proliferating FLT3ITD- TKD cells versus cells treated with midostaurin alone (Fig. 4E)." However, looking at Figs 4D and 4E, it appears that the effects of the midostaurin/SP600125 combination are virtually identical to SP600125 alone, and midostaurin provides no additional benefit. No p-values are provided to compare midostaurin+SP600125 to SP600125 alone but there seems to be no appreciable difference between the two by eye. In addition, the evaluation of synergism (versus additive effects) requires the use of specialized mathematical models (see for example Duarte and Vale, 2022). That said, I do not appreciate even an additive effect of midostaurin combined with SP600125 in the data presented.

      In my view, there are significant issues with clarity and detail throughout the manuscript. For example, additional details and improved clarity are needed, in my view, with respect to the design and readouts of the signaling perturbation experiments (Methods, p. 15 and Fig 2B legend). For example, the Fig 2B legend states: "Schematic representation of the experimental design: FLT3 ITD-JMD and FLT3 ITD-JMD cells were cultured in starvation medium (w/o FBS) overnight and treated with selected kinase inhibitors for 90 minutes and IGF1 and TNFa for 10 minutes. Control cells are starved and treated with PKC412 for 90 minutes, while "untreated" cells are treated with IGF1 100ng/ml and TNFa 10ng/ml with PKC412 for 90 minutes.", which does not make sense to me. The "untreated" cells appear to be treated with more agents than the control cells. The logic behind cytokine stimulation is not adequately explained and it is not entirely clear to me whether the cytokines were used alone or in combination. Fig 2B is quite confusing overall, and it is not clear to me what the horizontal axis (i.e. columns of "experimental conditions", as opposed to "treatments") represents. The Method section states "Key cell signaling players were analyzed through the X-Map Luminex technology: we measured the analytes included in the MILLIPLEX assays" but the identities of the evaluated proteins are not given in the Methods. At the same time, the Results section states "TKIs sensitive and resistant cells were subjected to 16 experimental conditions" but these conditions do not appear to be listed (except in Supplementary data; and Fig 2B lists 9 conditions, not 16). In my subjective view, the manuscript would benefit from a clearer explanation and depiction of the experimental details and inhibitors used in the main text of the paper, as opposed to various Supplemental files/figures. The lack of clarity on what exactly were the experimental conditions makes the interpretation of Fig 2 very challenging. In the same vein, in the PCA analysis (Fig 2C) there seems to be no reference to the cytokine stimulation status while the authors claim that PC2 stratifies cells according to IGF1 vs TNFalpha. There are numerous other examples of incomplete or confusing legends and descriptions which, in my view, need to be addressed to make the paper more accessible.

      I am not sure that I see significant value in the patient-specific logic models because they are not supported by empirical evidence. Treating primary cells from AML patients with relevant drug combinations would be a feasible and convincing way to validate the computational models and evaluate their potential benefit in the clinical setting.

    1. Ó˄oƒ†džś͛ǬĐŭr¾Ã ̈–Ʋ¦šŽÃŠϷ   LJR„  LJ|kl  LJärϺhrȻɆohNjĒñ˅oȸ„Ro]ϷÑǧΌrƆơlϷdžś͛ǬlǺϓr¾Ã ̈–ƲohNj̚ƤŠĬPdF

      7.This paper uses logos. As a whole, the analysis is objective, using many quotes and design suggestions. The discussion section also uses logos because it is derived from analysis rather than emotion.

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      6.The purpose of this paper is to clarify the characteristics of meta-landscape design and its evolution, following the planting plan of Tange et al. in the Peace Memorial Park. The research method is divided into two periods, from 1949 to 1955 and from 1970 to 1973, for analysis and discussion. The relationship between the north-south central axis and the landscape design, which is the key to the composition of Peace Memorial Park, and the expression of peace commemoration and memorialization, which is the theme of Peace Memorial Park, will also be discussed.

    Annotators

    1. En un corte de riñón fresco se observa con una coloración rojiza, debido a que una mayor cantidad de sangre (90 a 95%) se encuentra aquí. Esta región del parénquima renal se caracteriza por la presencia de glomérulos o corpúsculos renales que forman parte de la nefrona (figura 16-2).

    Annotators

    1. Screen\Nr i t i n g T o o l s • 4 5tagonist: Mildred Pierce, Citizen Kane, Ninotchka, Shane, Tootsie-the listis endless. Once in a while we encounter a story where two people wantmore or less the same thing and strive to achieve approximately the samegoal. Yet in these stories, sllch as Bonnie and Clyde, Butch Cassidy andthe Sundance Kid, and Some Like It Hot, the protagonist is usually theperson who makes the deci"sions that create the story. Clyde, Butch, andJoe/Josephine, while not having more screen time than their partners, dotake the role of the protagonist because they are the characters whoseactions the partner follows; it is their decisions that determine both characters' actions, and it is their desire that overwhelms the partner's desire.Only in the light of the protagonist's objective can a screen story beplotted, because the pursuit of that objective determines the course of theaction, however straightforward or deviolls the path may be. Here are thethree main points to remember about the objective:1. There can be only one main objective if the film is to have unity. Astory with a protagonist who has more than one ultimate aim mustinvariably dramatize the success or failure of one effort before goingon to the other, and this breaks the spine of the work and di ssipatesour interest. A screenplay is like a suspension bridge, with one endanchored in what the protagonist wants, and the other end anchored tothe disclosure of whether or not he gets it. A bridge that forks in themiddle, with branches leading to two different destinations, can neverbe structurally sound. (The fact that other characters also have desiresor objectives must not obscure the fact that the story we are followingis the pursuit of the protagonist's objective.)

      helps clarify why the major question of Dheepan was not family

    1. Author Response

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

      Reviewer 1

      One criticism the authors have made of previous studies was that they have not distinguished between 'tonic' and 'phasic' LC activity and could not demonstrate 'time- locked phasic firing'. This has not been achieved in the present report, as an examination of Fig 1 C,D and 2 C,D shows. Previous reports in rats and monkeys, using unit recording in rats and monkeys clearly show that the latency of LC 'phasic' responses to salient or behaviorally relevant stimuli are in the range of tens of milliseconds, with a very short duration, often followed by a long-lasting inhibition. This kind of temporal precision concerning the phasic response cannot be gleaned from the time scale shown in the Figures (assuming the time scale is in seconds). We can discern a long-lasting increase in tonic firing level for the more salient stimuli (Fig 1C) (although the authors state in the discussion that "we did not observe obvious changes in tonic LC-HPC activity). This calcium imaging methodology as used in the present experiments can give us a general idea of the temporal relation of LC response to the stimulus, but apparently does not afford the millisecond resolution necessary to capture a phasic response, at least as the data are presented in the Figures.

      While we understand the reviewer’s concern with our use of the terms phasic and tonic, we believe we have represented them as accurately as possible given our data. Unfortunately, the distinction between tonic and phasic activity is somewhat arbitrary, in that there is no strict definition, to our knowledge, of the exact parameters that activity must fall into to be categorized as tonic or phasic. While it is true that phasic LC activity has typically been studied with electrophysiological approaches that afford millisecond resolution and that observed phasic responses are often extremely short, there are numerous differences between those studies and this one. Most prominently, the stimuli used to elicit a phasic response are generally extremely short (often 1ms or less) and therefore generate extremely short phasic responses (Aston-Jones and Bloom, 1981a; Aston-Jones and Cohen, 2005), but this is not to say that phasic responses might not be longer in response to a longer lasting stimulus. Moreover, tonic activity is reported to track with behavioral state on the order of dozens of seconds to minutes and is not reported in response to specific stimuli (Aston-Jones and Bloom, 1981b). The “phasic” responses we report generally decay in less than 5 seconds in our fluorescence signals. Given the slow time course of decay for GcAMP6s (a single action potential can generate a response that lasts 3 or more seconds (Chen et al., 2013)) and the GRAB sensors (GRAB-DA2h τoff = 7.2s (Sun et al., 2020)), the underlying neural responses would have lasted for a significantly shorter period. Therefore, we believe the responses we observed are much more consistent with phasic responses to long-lasting sensory stimuli (20-second tone, 1-2 second shock), than with increases in tonic activity associated with a change in behavioral state. Finally, regardless of whether these responses are exactly the same as previously reported phasic responses, our photometry and optogenetics studies provide insight about a form of LC activity that is fundamentally different than what can be gleaned from much slower dialysis, lesion, and pharmacology studies. Nonetheless, we added the following to the discussion section to clarify the limitations of our interpretation:

      “…given their relatively short duration and the fact that they are elicited specifically by salient sensory stimuli, we refer to these responses as “phasic responses.” However, because of the comparatively slow dynamics of fluorescent sensors relative to electrophysiology, we cannot rule out the possibility that these responses are somehow different in nature to previously reported phasic LC responses. Thus, some care must be taken in conflating the characteristics and/or function of the relatively short-lasting responses presented here and the extremely fast phasic responses to very brief (μs to ms) sensory stimuli reported previously.”

      Much of the data presented here can be regarded as 'proof of concept' i.e. demonstrating that Photometric imaging of calcium signalling yields similar results concerning LC responses to salient or behaviorally relevant stimuli as has been previously reported using electrophysiological unit recording. The role of dopamine as the principal player in hippocampaldependent learning also corroborates previous reports.

      Although some of the data presented in this study could be seen as “proof of concept” or “confirmatory” of previous results, we believe this work extends previous results by showing 1) the importance of hippocampal dopamine to aversive hippocampus-dependent learning and trace fear conditioning specifically, 2) that LC responses are important at the specific times of learning (i.e. CS/US onset/termination), and 3) that dopamine in the hippocampus is likely important for learning in a way that is not tied to prediction error or memory consolidation.

      No attempt was made to address the important current question of the modular organisation of Locus Coeruleus, although the authors recognize the importance of this question and propose future experiments using their methodology to record simultaneously in several LC projection sites.

      While we do recognize the importance of this modular organization, which is addressed in the discussion as the reviewer mentions, experiments addressing this organization are beyond the scope of the present study. Future work will address the possibility that LC projections to different regions show differential responses during learning.

      The phasic-tonic issue has not been resolved by these experiments. Phasic responses of LC single units are short-latency, short-lived (just 3-4 action potentials), and followed by a relatively long refraction period. Multiunit responses will have a more jittery latency and longer-lasting response (but still only tens to hundreds of milliseconds). Your figures clearly show long-lasting increases in tonic firing levels, even though you state the contrary in the discussion. Therefore, I strongly recommend removing the word 'phasic' from the title.

      Addressed above.

      Yohimbine, the Alpha 2 antagonist, administered systemically, induces a massive increase in the rate of firing of LC cells (through blockade of autoinhibition at the cell body level at terminals). I guess its effect on the receptor 'backbones' overrides the massive release of NE and/or DA, but you might want to mention this; also include the dose of all drug treatments.

      Yes, yohimbine’s effect on the GRAB-NE signal is somewhat counter-intuitive given the known effect of yohimbine on norepinephrine levels. However, our result is consistent with previous reports (Feng et al., 2019). We have added the following to the results section to clarify:

      “Thus, even though yohimbine is known to increase NE levels in the hippocampus (Abercrombie et al., 1988), its blockade effect on the GRAB-NE sensor should result in a decrease in fluorescence after administration.”

      Include time scale units on all figures (I assume it is seconds in Figs 1 &2).

      Thank you for pointing out this issue, we have added units on all figures.

      • Is it possible to have a better quality example of staining? Fig 1 B in particular is very blurry. Is the yellow double staining? Please indicate. Most of the GCaMP seems to be outside the main area of TH staining. Fig 4 B is much nicer--and it looks morphologically, like LC.

      Unfortunately, the GcAMP6s staining was very dim in our hands and resulted in relatively blurry images. Yes, in this case, yellow is double staining. Regarding the morphology, the GCaMP image is taken from a sagittal section and the shape of expression is consistent with images of LC in the sagittal plane. However, given the quality of our ChR2 images, we are confident in the specificity of expression in these mice.

      Reviewer 2

      The claim that dopamine release in dHPC is caused by LC neurons is not directly tested. Unfortunately, the most critical experiment for the claims that dopamine release comes from LC during conditioning is not tested. A lack of dopamine signal in dHPC caused by inhibition of LC during TFC would show this. It is indeed an interesting observation that chemoegenetic activation of LC causes dopamine release in the dHPC. However, in the absence of concurrent VTA inhibition or lesion, it remains a possibility that the dopamine release is mediated through indirect actions on other dopamine-expressing neurons. The authors do a good job of arguing against this interpretation in the discussion, and the literature seems appropriate for this. However, the title is still an overstatement of the data presented in this study.

      We agree with the reviewer’s comments. As indicated in the discussion, it is possible that hippocampal dopamine is increased indirectly via LC projections to dopaminergic midbrain regions. We believe that our title is consistent with this possibility. When phasic stimulation was delivered to the LC, dopamine levels increased in the hippocampus and trace fear conditioning was enhanced. The observed increase in dopamine could be direct or indirect. As the reviewer notes, we argue for the former in the discussion section. A number of experiments would be needed to show this directly (record dopamine while: inhibiting the LC, inhibiting the VTA, stimulating LC while simultaneously inhibiting the VTA etc.) and we are planning to do these in the future.

      The primary alternative interpretations of the phasic activation experiment are whether only stimulation to the cue events (both on and off), or whether only stimulation to the shock. Thus this experiment would benefit from additional data showing either a no shock control, to show that enhanced activity of the LC to the tone is not inherently aversive, or manipulations to the tone but not to the shock.

      Future work will explore whether the contribution of LC to learning is primarily due to its activation during the CS or the US. However, this is beyond the scope of this manuscript.

      Specificity of the GRAB-NE and GRAB-DA sensors should be either justified through additional experiments testing the alternative antagonist (i.e. GRAB-NE CNO+eticloprode / GRAB-DA CNO+yohimbine) or additional citations that have tested this already. It is critical for the claims of the paper to show that these sensors are specific to dopamine or norepinephrine.<br /> Although sensitivity is a potential concern, these sensors have been thoroughly vetted and used by many groups since their generation. In particular, the creators of these sensors provided extensive data showing their specificity. The GRAB-DA sensor is ~10 fold more sensitive to DA than to NE (Sun et al., 2020, cited 239 times) and the GRAB-NE sensor is ~37 fold more sensitive to NE than to DA (Feng et al., 2019, cited 371 times).

      The role of dopamine in prediction error was tested through a series of conditions whereby the shock was presented either signaled (i.e. predicted), or not. However, another way that prediction error is signaled is through the absence of an expected outcome. Admittedly it might not be possible to observe a decrease in dopamine signaling with this methodology.

      Although this is a strong point, given that the study is not primarily focused on error prediction and the low likelihood of observing the typically small decrease in signaling during expected outcome omission, we feel that additional error prediction studies are beyond the scope of this manuscript. However, further experiments as suggested by the reviewer could prove interesting in future studies.

      The difference between Fig. 6E and 6H needs to be clarified. What is shown in Fig. 6E is that the response to the shock decreases through experience (i.e. by the 10th trial). However in Fig 6H, there is no difference between signaled and signaled shock, but this is during conditioning, and not after learning (based on my understanding of the methods, line 482).

      We are not sure we fully understand what point of clarification the reviewer is asking for. However, we have clarified in the methods that the signaled vs unsignaled shock experiment took place in animals that had already been trained on TFC. Thus, all of the trials took place after the animals had learned the tone-shock association. Therefore, although the drop in shock-response could be taken as an indicator of a prediction-error like signal, all the other data points to this not being the case (no change in tone response over training, no difference in signaled vs. unsignaled responses after training).

      Unless I missed it, at no point in the manuscript is the number of subjects described. Please add the n per experiment within each section describing each experiment in the methods (Behavioral procedures). Some more details in the photometry statistical analysis would be helpful. For example, what is the n per group for every data set that is presented? How many trials per analysis?

      We thank the reviewer for pointing this out. Animal numbers have been added in the methods section in the Behavioral Procedures, Optogenetics, and Drugs sub-sections and in the figure legends. Trial numbers are included in these sections and all trials were used for analysis.

      What is the difference in experimental procedure between Fig. 2D and Fig. 3B? It seems that they are the same, and yet the LC response to the conditioned CS is not.

      Fig. 3B is simply the Day 1 data from Fig 2D presented at a different scale because the shock response is included in Fig. 3B which necessitates a larger scale on both axes. Close inspection of the figures will show that the shapes of these two curves and the error around them is the same, but the different scaling obfuscates this slightly.

      Typo in the legend of Figure 2 - D should be E.

      Thank you, we have corrected this.

      • Anatomical localization of the virus injections, and more importantly the fiber placements, is not shown. Including this information helps with replication and understanding where exactly the observations were made in dHPC to contrast with prior studies.

      Representative examples are included in the manuscript in figure 1B, 3F, 4B, and 5B.

      Reviewer 3

      While the optogenetic study was lovely, a control using the same stimulation but delivered at different time points would have been a good addition to show how critical the neural signal at tone onset, tone offset, and shock is.

      We agree that it would be interesting in future studies to delineate the specific times when LC stimulation produces a learning enhancement. It could be that LC activity is most important during one specific time period (eg. just during shock) or that all three periods of activation are required. It would also be useful to know whether stimulation at other times during learning can produce an enhancement given the potentially long-lasting effects of dopamine on HPC plasticity and learning.

      Justification for the focus on D1 receptors was lacking.

      We chose to focus on D1 receptors because previous studies have shown that these receptors are critical for memory formation or consolidation in the hippocampus. We have added a sentence justifying this in the results section.

      “To test whether dopamine is required for trace fear memory formation, we administered the dopamine D1 receptor antagonist SCH23390 (0.1mg/kg) 30 minutes before training, as D1/D5 receptors have previously been shown to be critical for other types of hippocampus dependent memory and plasticity (Frey et al., 1990; Huang and Kandel, 1995; O’Carroll et al., 2006; Wagatsuma et al., 2018).”

      The manuscript provides convincing evidence that the neural signal is not an error- correcting one by including a predicted (by a tone) and unpredicted shock. One possibility is that perhaps the unpredicted shock could be predicted by the context. Some clarification on the behavioural procedures would help understand if indeed the unsignaled shock could be predicted by the context or not.

      Mice always exhibit freezing in the training environment, so the context is definitely a predictor of shock. However, the tone is a much better predictor because it is always followed by shock while the mice spend a large amount of time in the context without being shocked. This is demonstrated by the fact that the same procedure used in the current experiments consistently produces more tone fear than context fear (Wilmot et al., 2019). While we did not do long-term memory tests here, we assume the same dissociation occurred as it has been observed very consistently across studies (Chowdhury et al., 2005; Kitamura et al., 2014; Wilmot et al., 2019). Nonetheless, it is possible that a difference between signaled and unsignaled groups was obscured by the context. We should note however, that differences between dopaminergic responses to cued and uncued rewards and aversive outcomes has been observed and these animals were also trained in the same context (Eshel et al., 2016; Matsumoto and Hikosaka, 2009; Pan et al., 2005; Schultz, 1998). Therefore, we believe this experiment does differentiate the observed dopamine response in the hippocampus from previously reported VTA dopamine prediction error signaling.

      Figure 2 - tone termination in Tone only group - no change? Stats?

      Thank you for pointing out this omission. We have added the stats to the figure legend. Although the response to tone termination decreased numerically, it did not change significantly across days. This is one point we may seek to clarify in future studies, as the difference between tone onset and termination responses is unexpected. Given the relatively small responses, it’s possible future studies with stronger signal (eg. GcAMP8) may find differences in the tone termination response across training days. This is one of the reasons we focused primarily on the responses to tone onset and shock in the rest of the manuscript.

      Fig 4 data - stimulation at time incongruent with the signal as a control for the timing of stim.

      This is addressed above.

      Fig 5 - GRAB-NE - yohimbine seems to suppress the signal below the vehicle. Not the case for GRAB-DA. Is this sig? post-hoc stats?

      Yes, this does appear to be the case for GRAB-NE, and would not be entirely surprising given that there is likely a baseline level of NE (and dopamine) in the hippocampus that produces some degree of baseline fluorescence in the vehicle group. This signal could be reduced/abolished by blocking the sensor and preventing this baseline level of NE from binding and producing fluorescence. This may not be the same for the GRAB-DA for a variety of reasons – different sensor binding affinities, different baseline neurotransmitter levels, potentially non-equivalent drug doses, etc. Because of the large number of pairwise comparisons in this data (18), we did not make post-hoc pairwise comparisons.

      Shock response curve - lines 466-474 - some explanation of what the pseudorandom order of shock presentation means.

      We have added the following explanation to this section:

      “…pseudorandom order, such that the shocks did not occur in ascending or descending order or follow the same pattern in each block,…”

      Line 126 - the extinction came out of the blue, it needs some introduction such as a statement that the animals were exposed to extinction training following conditioning.

      We have added the following earlier in that same paragraph:

      “On the second and third days, mice underwent extinction trials in which no shocks were administered.”

      References in Response

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      Aston-Jones G, Bloom FE. 1981a. Nonrepinephrine-containing locus coeruleus neurons in behaving rats exhibit pronounced responses to non-noxious environmental stimuli. Journal of Neuroscience 1:887–900. doi:10.1523/JNEUROSCI.01-08-00887.1981

      Aston-Jones G, Bloom FE. 1981b. Activity of norepinephrine-containing locus coeruleus neurons in behaving rats anticipates fluctuations in the sleep-waking cycle. J Neurosci 1:876–886. doi:10.1523/JNEUROSCI.01-08-00876.1981

      Aston-Jones G, Cohen JD. 2005. AN INTEGRATIVE THEORY OF LOCUS COERULEUSNOREPINEPHRINE FUNCTION: Adaptive Gain and Optimal Performance. Annual Review of Neuroscience 28:403–450. doi:10.1146/annurev.neuro.28.061604.135709

      Chen T-W, Wardill TJ, Sun Y, Pulver SR, Renninger SL, Baohan A, Schreiter ER, Kerr RA, Orger MB, Jayaraman V, Looger LL, Svoboda K, Kim DS. 2013. Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499:295–300. doi:10.1038/nature12354

      Chowdhury N, Quinn JJ, Fanselow MS. 2005. Dorsal hippocampus involvement in trace fear conditioning with long, but not short, trace intervals in mice. Behavioral Neuroscience 119:1396–1402. doi:http://dx.doi.org/10.1037/0735-7044.119.5.1396

      Eshel N, Tian J, Bukwich M, Uchida N. 2016. Dopamine neurons share common response function for reward prediction error. Nat Neurosci 19:479–486. doi:10.1038/nn.4239

      Feng J, Zhang C, Lischinsky JE, Jing M, Zhou J, Wang H, Zhang Y, Dong A, Wu Z, Wu H, Chen W, Zhang P, Zou J, Hires SA, Zhu JJ, Cui G, Lin D, Du J, Li Y. 2019. A Genetically Encoded Fluorescent Sensor for Rapid and Specific In Vivo Detection of Norepinephrine. Neuron 102:745-761.e8. doi:10.1016/j.neuron.2019.02.037

      Frey U, Schroeder H, Matthies H. 1990. Dopaminergic antagonists prevent long-term maintenance of posttetanic LTP in the CA1 region of rat hippocampal slices. Brain Research 522:69–75. doi:10.1016/0006-8993(90)91578-5

      Huang YY, Kandel ER. 1995. D1/D5 receptor agonists induce a protein synthesis-dependent late potentiation in the CA1 region of the hippocampus. Proceedings of the National Academy of Sciences 92:2446–2450. doi:10.1073/pnas.92.7.2446

      Kitamura T, Pignatelli M, Suh J, Kohara K, Yoshiki A, Abe K, Tonegawa S. 2014. Island Cells Control Temporal Association Memory. Science 343:896–901. doi:10.1126/science.1244634

      Matsumoto M, Hikosaka O. 2009. Two types of dopamine neuron distinctly convey positive and negative motivational signals. Nature 459:837–841. doi:10.1038/nature08028

      O’Carroll CM, Martin SJ, Sandin J, Frenguelli BG, Morris RGM. 2006. Dopaminergic modulation of the persistence of one-trial hippocampus-dependent memory. Learning & memory 13:760–769.

      Pan W-X, Schmidt R, Wickens JR, Hyland BI. 2005. Dopamine Cells Respond to Predicted Events during Classical Conditioning: Evidence for Eligibility Traces in the Reward-Learning Network. J Neurosci 25:6235–6242. doi:10.1523/JNEUROSCI.1478-05.2005

      Schultz W. 1998. Predictive Reward Signal of Dopamine Neurons. Journal of Neurophysiology 80:1–27. doi:10.1152/jn.1998.80.1.1

      Sun F, Zhou J, Dai B, Qian T, Zeng J, Li X, Zhuo Y, Zhang Y, Wang Y, Qian C, Tan K, Feng J, Dong H, Lin D, Cui G, Li Y. 2020. Next-generation GRAB sensors for monitoring dopaminergic activity in vivo. Nat Methods 17:1156–1166. doi:10.1038/s41592-02000981-9

      Wagatsuma A, Okuyama T, Sun C, Smith LM, Abe K, Tonegawa S. 2018. Locus coeruleus input to hippocampal CA3 drives single-trial learning of a novel context. Proceedings of the National Academy of Sciences 115:E310–E316. doi:10.1073/pnas.1714082115

      Wilmot JH, Puhger K, Wiltgen BJ. 2019. Acute Disruption of the Dorsal Hippocampus Impairs the Encoding and Retrieval of Trace Fear Memories. Frontiers in Behavioral Neuroscience 13. doi:10.3389/fnbeh.2019.00116

    1. While sharing the details of CIs (created using RBL bank) with the customers, ensure that the fifth character in the IFSC is number 0 and not the letter O. For example, valid IFSC is RATN0VAAPIS and not RATNOVAAPIS.

      The image attached below will also change. The current image has a UPI ID as well.

    1. El desarrollo del derecho romano se ha clasificado en diferentes perio-dos que van desde la fundación de Roma hasta el Imperio de Justiniano; encada uno de ellos hay rasgos particulares que los distinguen; sin embargo,para este estudio, es de suma importancia conocer las fuentes del derechoen general, ya que es a través de éstas que se puede señalar si existe, o no,una división entre derecho público y derecho privado.Es importante señalar cuáles son los periodos 1 en los que se clasifica lahistoria del derecho romano, ya que a través de éstos se formaron sus ca-racterísticas y, principalmente, donde se encuentra el fundamento de laclasificación romanista del derecho en público y privado, división que,como ya se dijo, habría que analizar si aún subsiste o si en la actualidadsólo se trata de una clasificación meramente didáctica.1. Derecho romano arcaico. Desde la fundación de Roma, 753 a. C.,hasta la promulgación de las leyes de las XII Tablas, 449 a. C.2. Derecho romano preclásico. Desde la promulgación de las Leyes delas XII tablas, 449 a. C., hasta el final de la República, 27 a. C.3. Derecho romano clásico. Desde el final de la República, 27 a. C.,hasta el imperio de Alejandro Severo, 235 d. C.4. Derecho romano posclásico. Desde Alejandro Severo, 235 d. C., hastaJustiniano, 527 d. C.

      En primera instancia esta es una introducción clara y estructurada sobre los antecedentes del desarrollo del derecho romano, destacando la importancia de comprender las fuentes del derecho en general para poder discernir entre el derecho público y el derecho privado.

    1. se crearon normas decastigo o sanción que garantizarán una convivencia correcta entre losindividuos

      Esto es algo muy importante para vivir en sana convivencia dentro de la sociedad, si no existirán estas normas seria un caos total.

    2. El deber es la obligación que toda persona tiene que cumplir pararealizar un mandato, dicho en otras palabras, es el hacer o no hacer unadeterminada conducta, de lo contrario se aplicará una sanción

      Este fragmento nos presenta con claridad lo que le compete al derecho con los deberes y que tienen una consecuencia los actos inapropiados en este caso una sanción correspondiente.

    1. La rama del derecho público y su clasificaciónDe acuerdo a la Teoría Romana el derecho se divide en dos grandes ramas: elderecho público y el derecho privado. El Derecho Público es el que atañe a laconservación de la cosa romana y privado el que concierne a la utilidad de losparticulares

      Me parece un tema muy interesante, ya que no sabia que habia tantas ramas en el derecho, las cuales son fundamentales para poder regular la convivencia social o establecer normas de conducta, en estas páginas se explica muy bien cada una de ellas.

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