Welcome to the NBO results for propargyl silane! Atom numbering in the molecule is as shown below. Silicon is atom 1; that's tough to see. Most important is that carbons 3 and 4 are triply bonded and carbon 3 is the internal carbon.

Welcome to the NBO results for propargyl silane! Atom numbering in the molecule is as shown below. Silicon is atom 1; that's tough to see. Most important is that carbons 3 and 4 are triply bonded and carbon 3 is the internal carbon.

Of the people of Henna (modern Enna)

SciScore for 10.1101/2022.01.12.22269192: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2022.01.11.475922: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32, 26, 28 and 30. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

both of these references appear to be the same, and if so, why not have just the one reference?

Stock, S. J., Carruthers, J., Calvert, C., Denny, C., Donaghy, J., Goulding, A., Hopcroft, L. E. M., Hopkins, L., McLaughlin, T., Pan, J., Shi, T., Taylor, B., Agrawal, U., Auyeung, B., Katikireddi, S. V., McCowan, C., Murray, J., Simpson, C. R., Robertson, C., … Wood, R. (2022). SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland. Nature Medicine, 1–9. https://doi.org/10.1038/s41591-021-01666-2

This is the profile for Mark Hughes (0000-0002-2168-0514). Up until now I've been generating my own linked data version of ORCID records that look very similar to this, but going forward this will simplify life.

Note that I've truncated the above example, it's actually this:

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  "@type": "Person",
  "@id": "https://orcid.org/0000-0002-2168-0514",
  "mainEntityOfPage": "https://orcid.org/0000-0002-2168-0514",
  "givenName": "Mark",
  "familyName": "Hughes",
  "affiliation": {
    "@type": "Organization",
    "name": "Royal Botanic Garden Edinburgh",
    "identifier": {
      "@type": "PropertyValue",
      "propertyID": "RINGGOLD",
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        "name": "A revision of Begonia sect. Petermannia on Sumatra, Indonesia",
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        "name": "Further discoveries in the ever-expanding genus Begonia (Begoniaceae): fifteen new species from Sumatra",
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This gives us a list of Mark's publications from ORCID. If there aren't any publications listed, the @reverse property is empty. Note that @reverse is a JSON-LD trick that enables the JSON-LD document to include not only things linked from Mark's ORCID id (e.g., his name and affiliation) but also things his ORCID id is linked to (e.g., that he is the author of works such as https://doi.org/10.1017/s0960428619000283).

SciScore for 10.1101/2022.01.10.475620: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Our study presents limitations. The use of fluorescent tetramers in ICS/flow cytometry analyses would have identified SARS-CoV-2-specific CD8+ T cell sub-populations more accurately. In addition, challenging immunized mice with sub-lethal viral doses may have revealed potentially protective effects induced by S1-specific CD8+ T cells also. Furthermore, the lack of quantification of viral loads in lungs of protected mice precluded the evaluation of the effects of N-specific immunity on viral spread within airway tissues. Emergence of variants against which anti-S neutralizing antibodies lose potency represents one of the most relevant shortcoming for current anti-SARS-CoV-2 vaccines. Notably, N-specific antiviral CD8+ T cell immunity is not expected to suffer from such a limitation. In fact, as reported in fig. 7, amino acid sequences of N protein from current variants of concern (VOCs) are well conserved, at least in part because mutations in this key viral component could have detrimental effects on optimal viral fitness. By consequence, the N-specific CD8+ T cell immune response against a single viral strain is anticipated to be effective also against other VOCs. In addition, based on the observations on patients recovered from SARS-CoV infection [11], SARS-CoV-2 N-specific CD8+ T cell immunity would wane with a kinetics much slower than that of anti-S neutralizing antibodies. We here demonstrate that adequate levels of N-specific CD8+ T cell immunity correlate with protect...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

Olson, S. M., Newhams, M. M., Halasa, N. B., Price, A. M., Boom, J. A., Sahni, L. C., Pannaraj, P. S., Irby, K., Walker, T. C., Schwartz, S. P., Maddux, A. B., Mack, E. H., Bradford, T. T., Schuster, J. E., Nofziger, R. A., Cameron, M. A., Chiotos, K., Cullimore, M. L., Gertz, S. J., … Randolph, A. G. (2022). Effectiveness of BNT162b2 Vaccine against Critical Covid-19 in Adolescents. New England Journal of Medicine, 0(0), null. https://doi.org/10.1056/NEJMoa2117995

SciScore for 10.1101/2022.01.09.22268975: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

This limitation is especially pronounced in ICUs for patients requiring mechanical ventilation (17). It is necessary to develop a scoring system that can be used by physicians, to estimate the severity of the disease and prognosis of each patient at an early stage of the disease, which will grant a wider timespan for interventions. This tool also helps to reduce hospital care costs and improves its quality in the health care units (18-20). In this survey, we designed a simplly calculated clinical risk score, by using the patient’s clinical characteristics and laboratory data, which can be used as a predictor to estimate the severity of the disease, the need for hospitalization, and the possibility of ICU admission requirement during hospitalization. Low DBP (≤ 75 mmHg), prolonged PT (> 16.2s), increase in the level of LDH (> 731 U/L), BUN >23mg/dl, elevated CRP (> 73.1 mg/L), and decrease in oxygen saturation (<84%) were detected as risk factors for disease severity among 480 adult patients. Using this scoring system is a useful strategy for screening high-risk patients in crowded care centers during the COVID-19 outbreak. Severe hypoxemia (O2 sat<84%) had the highest odds ratio (OR= 9.19) among the 6 risk factors determining the severity of the disease in our survey. This finding was consistent with a cohort study by Bahl et al. among 1461 patients in which O2 sat of ≤188% was associated with a higher mortality rate (21). In the review conducted by Petrilli et al. among 4103...

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SciScore for 10.1101/2022.01.09.22268986: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

The present study has both strengths and limitations. By implementing this immunological survey in a community-based cohort study with a wide age range of healthy Japanese people who had been unexposed to SARS-CoV-2, we were able to collect preliminary but unprecedented epidemiological data regarding the prevalence and levels of assumable polyreactive natural salivary IgA autoantibodies that exhibit reactivity with the virus. To the best of our knowledge, our survey, along with the preceding one (38), is the only available study which has provided data useful for considering a putative role mucosal natural IgA antibodies in protecting the human host from SARS-CoV-2 infection. Supportably, the presence of natural polyreactive sIgA autoantibodies acting as the frontline of mucosal defense against various infections has been demonstrated (59). Our study has several limitations. Firstly, our sample size was not large with limiting the robustness of our findings in saliva, as well as in serum. If such samples could be increasingly available, statical power for the analyses presented here will be increased. Secondly, we do not know whether and what levels of the salivary IgA detected in the presented study are protective through neutralization against SARS-CoV-2 infection. Thirdly, because of the lack of follow-up data, it was also unable to directly correlate negativity for or low levels of SARS-CoV-2-reactive salivary IgA with the feasibility to have the virus infection. Neverthe...

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SciScore for 10.1101/2022.01.08.22268944: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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Fernandez-Castaneda, A., Lu, P., Geraghty, A. C., Song, E., Lee, M.-H., Wood, J., Yalcin, B., Taylor, K. R., Dutton, S., Acosta-Alvarez, L., Ni, L., Contreras-Esquivel, D., Gehlhausen, J. R., Klein, J., Lucas, C., Mao, T., Silva, J., Pena-Hernandez, M., Tabachnikova, A., … Monje, M. (2022). Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain (p. 2022.01.07.475453). https://doi.org/10.1101/2022.01.07.475453

Frenzel, S. B., Junker, N. M., Avanzi, L., Bolatov, A., Haslam, S. A., Häusser, J. A., Kark, R., Meyer, I., Mojzisch, A., Monzani, L., Reicher, S., Samekin, A., Schury, V. A., Steffens, N. K., Sultanova, L., Van Dijk, D., van Zyl, L. E., & Van Dick, R. (2022). A trouble shared is a trouble halved: The role of family identification and identification with humankind in well-being during the COVID-19 pandemic. British Journal of Social Psychology, 61(1), 55–82. https://doi.org/10.1111/bjso.12470

Tseng, H. F., Ackerson, B. K., Luo, Y., Sy, L. S., Talarico, C., Tian, Y., Bruxvoort, K., Tupert, J. E., Florea, A., Ku, J. H., Lee, G. S., Choi, S. K., Takhar, H. S., Aragones, M., & Qian, L. (2022). Effectiveness of mRNA-1273 against SARS-CoV-2 omicron and delta variants (p. 2022.01.07.22268919). https://doi.org/10.1101/2022.01.07.22268919

SciScore for 10.1101/2022.01.05.475037: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Limitations of the study: ZCB11 probably represents the broadest breadth among bNAbs reported thus far with comparable potency against all current SARS-CoV-2 VOCs including Omicron and OmicronR346K. We are still in the process in determining its mode of action by solving structures of the RBD-ZCB11 Fab complex. Such information will be useful to guide vaccine design as mentioned because the frequency of elite vaccine remains low (2/34 in this study). To understand the frequency of ZCB11-like bNAb among BNT162b2-vaccinees, we need to investigate other elite responders who show equally potent bNAb responses. More ZCB11-like bNAbs should be also discovered to improve current antibody-based cocktail immunotherapy. For animal challenge experiments, we have done a single dose efficacy experiment. Different doses and routes of administration or antibody combination will be tested in future experiments to provide useful information to support clinical development of ZCB11 and ZCB11-like bNAb.

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Douaud, G., Lee, S., Alfaro-Almagro, F., Arthofer, C., Wang, C., McCarthy, P., Lange, F., Andersson, J. L. R., Griffanti, L., Duff, E., Jbabdi, S., Taschler, B., Winkler, A. M., Nichols, T. E., Collins, R., Matthews, P. M., Allen, N., Miller, K. L., & Smith, S. M. (2021). Brain imaging before and after COVID-19 in UK Biobank (p. 2021.06.11.21258690). https://doi.org/10.1101/2021.06.11.21258690

SciScore for 10.1101/2022.01.04.474979: (What is this?)

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SciScore for 10.1101/2022.01.03.474825: (What is this?)

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SciScore for 10.1101/2022.01.03.22268599: (What is this?)

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SciScore for 10.1101/2022.01.03.21268111: (What is this?)

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DOI: 10.1016/j.devcel.2021.12.008

Resource: Leica DMI6000 B inverted microscope (RRID:SCR_018713)

Curator: @scibot

SciCrunch record: RRID:SCR_018713

What is this?

Author Response

Reviewer #1 (Public Review):

In Wang et al., the authors investigate issues related to the relative proportion of flux for the enzymatic decarboxylation of pyruvate between PDH (pyruvate dehydrogenase) and PFOR (pyruvate-ferredoxin oxoreductase) in the model organism Synechococystis. The manuscript provides evidence that PDH becomes increasingly inactivated by a high ratio of NADH:NAD+ as well as evidence to suggest that PFOR is transcribed and remains intact under aerobic conditions. The authors put forward the theory that both PDH and PFOR are functionally active routes for pyruvate decarboxylation under aerobic conditions, whereas PFOR has previously been assumed to be inactive under growth conditions containing oxygen. This distinction is particularly highlighted by conditions where Synechocystis is grown photomixotrophically - and where the NADH:NAD+ pool may be relatively over-reduced because of two parallel inputs of reductant (water-splitting at PSII and catabolism of glucose). The authors examine growth under photoautotrophic and photomixotrophic conditions for a number of relevant mutants including members of the ferredoxin/flavodoxin family, PFOR, and NDH-1 complex subunits.

The theory put forward in this manuscript is of general interest regarding electron flux through the combined electron transport chain (photosynthetic + respiratory) of cyanobacteria. The authors further broaden the potential audience for the manuscript by elaborating on the potential significance of these results in the context of a switch from PFOR (ancestral) to PDH (oxygenic/modern).

Comments:

Generally, theories put forward in this manuscript are intriguing and have a number of potential implications for understanding electron flux and regulation of central metabolic processes in photosynthetic microorganisms. If these theories are supported and become more generally adopted, they would have significant impact on the understanding of the regulation of central carbon metabolism in cyanobacteria. That said (due in no small part to the complexity of some of these pathways), the evidence provided to support the hypotheses is indirect in many instances. In some cases, there is a pairing of indirect data with broad statements that can come across as over-reach. These problems can be somewhat exacerbated by an unclear organization at parts of the Discussion, a lack of succinctly defined claims, and numerous typographical considerations.

Thank you very much for this point. We now reorganized the discussion and overhauled it completely. It starts with aspects that are best supported by our data. We then added two sentences to stress that the following lines include hypothetical considerations that are meant as thought-provoking impulses. We hope that thereby over-reach is prevented.

Major considerations:

A major component of the proposed theories in this manuscript rest upon the assumption that PFOR is an active enzyme under highly aerobic conditions: this claim is never directly demonstrated.

This is true. We could show though that PFOR of Synechocystis is in constrast to most bacterial PFORs stable in the presence of oxygen. However, as stated likewise for the oxygen stable PFOR of the obligate aerobe Sulfolobus acidocaldarius (3), and PFOR from E. coli, which was recently shown to contribute to metabolism in the presence of oxygen in vivo (1) we as well had to remove oxygen for enzyme acitivty in vitro. This point is discussed frankly.

Indirect evidence of altered growth of pfor mutants, increased repression of PDH, and the higher NADH:NAD+ ratio under photomixotrophic conditions is in general alignment with this theory. However, while deletion of pfor does indeed result in altered growth dynamics in Synechocystis under periods of photomixotrophy, the alterations do not entirely align with the idea that this pathway is critical for rapid growth under aerobic conditions. For instance, pfor and most of the highlighted mutants (fdx 3, fdx 9, isiB) presented in Figure 3 show the greatest defects in their OD after reaching stationary phase (more rapid decline in OD on/after Day 6) relative to WT. This doesn't align as nicely with the highest NADH:NAD+ seen in Days 3-5 (which is also specifically called out: e.g., Line 146, Supplemental Figure S8).

We are very cautious to compare growth experiments day by day. This is due to the fact that the growth behaviour of WT and mutants differ between experiments. We therefore repeat these experiments in several independent experiments including at least three replicates and show the data of typical growth experiments. In the case of the shown growth behaviour of WT and pfor and the NADH/NAD+ ratios under photoautotrophic and photomixotrophic conditions shown in figure 1, NADH/NAD+ ratios were determined in exactly those cultures for which growth data are shown. It is therefore legitimate to directly compare these results day by day. However, we did not determine the NADH/NAD+ ratios of the cultures shown in Fig. 3. The rise in NADH might have started with a delay here.

In this context, the deletion of F-GOGAT is much more convincing in it's severity and timing, yet for this mutation to have a more severe phenotype is unexpected if PFOR is one of the primary/sole electron donors to the ferredoxin pool from glucose utilization as proposed (i.e., stated differently, F-GOGAT is only one of the enzymes downstream of ferrodoxin and might be expected to have a more subtle phenotype in comparison to the KO of PFOR if that is a primary source for electrons to ferredoxin under photoheterotrophic conditions).

F-GOGAT requires reduced ferredoxin which can be provided by PFOR and in addition also by PSI. As electrons from glucose oxidation can be fed via photosynthetic complex I into the PQ-pool they will eventually arrive at PSI (Fig. 3C) where ferredoxin can be reduced and transfer electrons to F-GOGAT. However, to get a truly complete picture of the situation several issues will have to be addressed in the future: we do not know which of the low abundant ferredoxins as well as high abundant ferredoxin 1 interact with PSI, F-GOGAT, PFOR and photosynthetic complex I. It would be furthermore helpful to know all midpoint potentials of the different ferredoxins. Without this information it might be too much to ask for a simple interpretation.

A central tenant of the argument put forward on the evolutionary importance of using either PFOR vs. PDH is the conservation of extra free energy by the former reaction. However, additional information on the ferredoxin paralog(s) that accept electrons from PFOR is necessary to evaluate these claims. Based on the data within these manuscripts, Fdx3, Fdx9, and IsiB have the strongest links to PFOR: though the authors do take care to never state directly that they have evidence that these are the acceptors in vivo. Given the variability in the midpoint potentials of different ferredoxins, some ferredoxin acceptors may better conserve the free energy in pyruvate, while others may actually be more 'wasteful' than NAD+ as the acceptor through PDH. Unfortunately, the midpoint potentials for Fdx3, Fdx9, and IsiB are unknown or not stated in this manuscript. It is therefore unclear what ferredoxin is being used as the reference point for conservation of Gibbs free energy in Figure 4C and referenced multiple times in the text.

We agree that it would be great if we already knew the redox potentials of all the ferredoxins involved. We are currently working on this issue. All that we know for now is that the redox potentials of ferredoxins lay between -240 mV to -680 mV whereas the redox potential is around -320 mV for NAD(P)H/NAD(P)+. Unpublished data that require further validation reveal that the redox potential of Fdx9 is definitely more negative than the redox potential of Fdx1 (-412 mV) in Synechocystis and is thereby clearly more negative that -320 mV. However, as these data require further validation, we did not name numbers. In addition, interaction studies on PFOR and low abundant ferredoxins are planed and preparations are in progress.

Finally, the measurements of NADH:NAD+ (most prominently used for measurements in Fig 1B) utilized kits that require multiple, long centrifugation steps in the dark prior to assaying this rapidly exchanging pool. While it appears that the authors were able to get reproducible results with these kits, it is difficult to interpret what the increase in relative NADH levels in glucose-fed cells means given that 10+ minutes of incubation in the dark and/or changing temperatures elapsed after the cyanobacteria were removed from the incubator before the NADH:NAD ratio was assessed. While it superficially makes logical sense that the cytosol would be over-reduced when illuminated and under glucose feeding relative to illumination alone, it shouldn't be assumed that these measurements are representative of this rapidly-exchanging pool under the steady-state growth conditions.

Thank you very much for raising this important point. We are very much aware of the difficulties to determine the redox state of NADH:NAD+ using these kits. However, there is no other method available that properly distinguishes NADH and NADPH. Furthermore, the centrifugation step was done at -9°C which should minimize metabolic reactions during this step. However, we now added in vivo measurements using the NAD(P)H-module available for the PAM and using the Dual-KLAS/NIR to determine the redox state of ferredoxin (newly added Fig. S4). Both methods show that NAD(P)H as well as ferredoxin are more strongly reduced under photomixotrphic conditions in comparison to photoautotrophic conditions and thus support our previous data.

Reviewer #2 (Public Review):

The observation that cyanobacteria can use two alternative pyruvate decarboxylating enzymes using either NAD+ or ferredoxin is an interesting and the work is useful contribution. The authors very nicely characterize the enzymatic properties of the two pyruvate metabolizing enzymes and also are able to connect the ideas of redox balance with a set of ferredoxins. Even though they are not able to definitively characterized the specific ferredoxin which interacts with the enzyme, the analysis is nicely conducted and it's clear that the suggestion they're making regarding the involvement of the minor ferredoxins is compelling. However, the work could be written in a way that might be more useful.

Specific comments:

Overall this is an interesting study, but the arguments could be sharpened and better connected with the literature. The introduction needs to be considerably revised in my opinion. It is not obvious whether it is even appropriate to discuss the enzymes as an aerobic enzymes or aerobic enzymes, since this concept is simplistic and perhaps, archaic. Indeed, placing the results of the present study in the context of "aerobic enzymes versus aerobic enzymes" is a bit of a 'strawman' argument. For example, the counter examples of O2-tolerant enzymes cited seem to suggest that PFORs have been capable of evolving into O2-tolerant enzymes quite readily and that two types of decarboxylase have evolved for quite different reasons than simple replacement for a new environment. Instead, I think a more current and general perspective relates more to the interpretation that the authors are already putting forth. Namely, the enzymes are utilized according to redox balance considerations rather than sensitivity to oxygen.

Therefore, I think the very long and pedantic introduction is useful for review, but only if it is shortened and also includes the alternative interpretation regarding adaptations to redox potential in the cytoplasm. My guess is that there are plenty of examples of redox balance function arguments in the literature to refer to in contrast to the evolutionary replacement argument used. Certainly, there are good examples regarding glucose toxicity in mutants of Synechocystis that can be considered.

Thank you very much for this point. The O2-tolerant PFORs mentioned were merely shown to be stable in the presence of oxygen in vitro which means that they can be isolated under anaerobic conditions. However, all enzymatic in vitro assays required anaerobic conditions. Only one PFOR was shown to be active in the presence of oxygen in vitro. Physiological studies on the importance of these enzymes under aerobic conditions in vivo are completely missing. However, animated by the requests of the reviewers we searched the literature intensively again and indeed found a recent report, which describes the involvement of PFOR in redox regulation in an aerobic culture of an E. coli mutant, in which glucose-6P dehydrogenase (ZWF) was down-regulated (1). We included this study both in our introduction and discussion. It very much supports our own findings, as the E. coli PFOR requires likewise anoxic conditions in in vitro enzyme tests. We agree that the idea that PDH complex and PFOR are exclusively regulated by oxygen availability might sound simplistic. However, we do not fully agree that this is a strawman argument as both enzyme systems are still mostly discussed as counterparts for either aerobic respiration (PDH complex) or anaerobic fermentation (PFOR)(4). To the best of our knowledge, the study that was included now and our own data, are the very first ones that put clearly forward the idea, that redox control governs the activity of these enzyme systems at the pyruvate node independent of oxygen. However, doubts about the rather simplistic distinction between aerobic versus anaerobic enzymes in general have indeed been expressed. Even though these studies in general lack physiological in vivo experiments. We therefore included this information in the introduction as well. (line 76: There are several reports on the aerobic expression of enzymes that are assigned to anaerobic metabolism in prokaryotes and eukaryotes and therefore challenge the simplistic distinction between aerobic versus anaerobic enzymes (5-7). Their physiological significance and regulation are only partly understood.) This did not result in a shortened introduction though as additional information was added. The new introduction thus includes alternative interpretations as requested and is therefore hopefully more balanced.

Given the interpretation that the alternative forms of the enzyme help cells adjust their redox balance to different conditions, such as photomixotrophic growth, the very nice enzymatic analysis and growth studies of the mutants work would be significantly strengthened by more direct physiological measurements that report intracellular redox states.

Thank you very much for this important point. Intracellular redox states were shown by measurements of the NAD+/NADP level (Figure 1B) and were now extended by new in vivo measurements that show that both the NAD(P)H and the ferredoxin pools are more reduced under photomixotrophic in contrast to photoautotrophic conditions (new Fig. S4).

Minor comments:

line 211: Perhaps, "..the deleted alleles failed to segregate, keeping some wild type copies."

This was changed to: the deleted alleles of fx2 (sll1382) and fx5 (slr0148) failed to segregate, keeping some wild type copies.

It would be interesting to characterize whether the observed distribution of PFOR correlates with specific physiological features. In other words, PFOR seems to become important upon the addition of an external carbon source in way that must integrate with autotrophic metabolism (i.e. mixotrophic growth) altering the balance of the oxidized and reduced form of redox cofactors--does the observed distribution correlate at least with the metabolic characteristics of the handful that have been studied in the lab?

Thank you very much for this suggestion. We checked the lists of cyanobacteria that either possess or do not possess a PFOR in order to search for shared known physiological features. However, the challenge is currently that the number of uncharacterized cyanobacteria in our list is too large. It is therefore impossible to find solid correlations. But we fully agree that it would be interesting to find these.

A more detailed set of calculations that help explain panel C in figure 4 need to be included to support the quoted values for redox potential in free energy. I assume these are standard values and and the specific superscripts and subscription associate with the ΔG nomenclature needs to be defined.

The calculations are shown in the materials and methods part. A respective notice (for calculations see materials and methods part) is now given in the legend of Fig. 4C. Information concerning the nomenclature is found in the cited literature in the materials and methods part as well.

Reviewer #3 (Public Review):

The manuscript by Wang et al. conclusively demonstrates that the cyanobacterium Synechocystis sp. PCC6803 prefers to use the ferredoxin-reducing enzyme PFOR over the NAD+-reducing PDH-pathway when grown under photomixotrophic conditions while the PDH-route is favored under photoautotrophic conditions. Both the potential physiological meaning of this switch and implications for the evolutionary history of the role of the respective enzymes and their pathways are discussed.

The main hypothesis of this work considers that PFOR-mediated decarboxylation of pyruvate replaces the PDH-based one when cells shift from photoautotrophic to photomixotrophic growth conditions. This hypothesis is assessed via the comparison of growth curves measured on a host of deletion mutants and via direct detection of expression levels of certain enzymes. The authors' hypothesis is robustly supported by the majority of the reported experiments and the reviewer is fully convinced by these data. However, I would hold that the data shown with respect to phosphorylation of PDH (Fig. S4) are unconvincing. I can't see a clear difference in growth-curves for the incriminated mutants deltaspkB and L which would convincingly exceed the variation observed for the entire dataset.

We agree that the data on the phosphorylation of the PDH complex including the kinase mutants are not very convincing. We were uncertain from the beginning on whether it would be a good idea to include these data sets and therefore discussed them very cautiously in the manuscript. Anyway, as the enzymatic tests with the E3 subunit of the PDH complex at different NADH concentrations show convincingly that high NADH levels have an inhibitory effect on the complex, we now decided to delete both data sets out of the manuscript, as they are not really required for the statement of the manuscript.

1) S. Li et al., Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli. Metab Eng 64, 26-40 (2021).

2) T. Nakayama, S. Yonekura, S. Yonei, Q. M. Zhang-Akiyama, Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK - regulation of expression and biological roles in protection against oxidative stress. Genes Genet Syst 88, 175-188 (2013).

3) A. Witt, R. Pozzi, S. Diesch, O. Hädicke, H. Grammel, New light on ancient enzymes – in vitro CO2 Fixation by Pyruvate Synthase of Desulfovibrio africanus and Sulfolobus acidocaldarius. The FEBS Journal 286, 4494-4508 (2019).

4) M. Müller et al., Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiology and Molecular Biology Reviews 76, 444 (2012).

5) S. B. Gould et al., Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance. Proceedings of the Royal Society B: Biological Sciences 286, 20191491 (2019).

6) O. Schmitz, J. Gurke, H. Bothe, Molecular evidence for the aerobic expression of nifJ, encoding pyruvate : ferredoxin oxidoreductase, in cyanobacteria. FEMS Microbiol. Lett. 195, 97-102 (2001).

7) K. Gutekunst et al., LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator. Molecular Microbiology 58, 810-823 (2005).

SciScore for 10.1101/2021.12.30.21268540: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04331899</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Single-Blind Study of a Single Dose of Peginterferon Lambda-…</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.30.21267140: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

No key resources detected.

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

12 Limitations are associated with the analytic approach herein. The exploratory analysis of CRP as it relates to the primary endpoint of the likelihood of achieving SWOV was pre-specified, all other analyses were post-hoc, and none were prospectively powered. Therefore, the results should be interpreted with this caveat in mind. The findings herein will be further evaluated in the NIH-sponsored ACTIV-5/BET-B trial, that includes lenzilumab and where the primary efficacy analysis prospectively evaluates incidence of IMV, ECMO, or death in participants with baseline CRP<150 mg/L. In summary, this comprehensive analysis of LIVE-AIR CRP data provides evidence for the utility of CRP to predict progression to IMV and death. GM-CSF neutralization with lenzilumab significantly improved SWOV in adults hospitalized with COVID-19 pneumonia compared to placebo. Those participants who had baseline CRP levels <150 mg/L responded more favorably to lenzilumab treatment, than those with CRP>150 mg/L. These finding suggest that CRP may be a useful biomarker in determining which participants may be most successfully treated with lenzilumab.

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04351152</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Phase 3 Study to Evaluate Efficacy and Safety of Lenzilumab …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04280705</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Adaptive COVID-19 Treatment Trial (ACTT)</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.29.474471: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

A primary limitation in SARS-CoV-2 research is the high risk associated with working with a pathogenic respiratory pathogen, in terms of both the availability of suitable facilities and of suitably trained researchers. Here we present a range of approaches to facilitate research into all facets of SARS-CoV-2 replication, including cell entry, nucleic acid transcription and replication, and virus assembly and release; collectively these systems are tools to identify and characterize inhibitors at any point in SARS-CoV-2 replication. These systems are based on subgenomic SARS-CoV-2 replicons carrying reporter genes, reducing biological hazards and providing means to easily measure viral replication. The most popular strategy for generating replicons from positive-strand RNA virus is to transcribe RNA in vitro that can be electroporated into target cells to initiate replication. To facilitate use of the assay, particularly in the context of large-scale screening, we eliminated the need for in vitro transcription by cloning cDNA for the SARS-CoV-2 replicons into a BAC under control of a CMV promoter. The replicon comprised all replication-essential proteins and sequences but omitted the structural proteins S, E, and M; additionally, reporter genes were included as a separate ORF using the TRS-B of M to drive production of the sgRNA expressing the reporter cassette. Placing the reporter cassette in a sgRNA ensured that formation of a functional RTC was essential for reporter gene ...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04960202</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">EPIC-HR: Study of Oral PF-07321332/Ritonavir Compared With P…</td></tr></table>

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

Swire-Thompson, B., Cook, J., Butler, L. H., Sanderson, J. A., Lewandowsky, S., & Ecker, U. K. H. (2021). Correction format has a limited role when debunking misinformation. Cognitive Research: Principles and Implications, 6(1), 83. https://doi.org/10.1186/s41235-021-00346-6

SciScore for 10.1101/2021.12.27.21268459: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.28.474336: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

A limitation of the WA1/2020 UVC in a Delta heterologous challenge was the absence of any meaningful protection in nasal swabs. This discordance between vaccine variant, versus virus variant, is the principal challenge facing current vaccinated populations and might suggest the reason for ongoing infectious spread but more limited morbidity and mortality against these emerging variants29, 31. As regards duration of protection, the theoretical hyper-immunity postulated by creating a self-adjuvanting, hyper-immune UVC established robust initial nAb titers. When these animals were rechallenged 6-month later, the nAb response stayed robust at the higher, and now established for clinical use, 1e8 UVC dose. Moreover, the persistent nAb response at 6-months remained robust for SARS-CoV-2 WA1/2020, Beta and Delta variants. As regards intrinsic safety, the UVC undergoes lethal irradiation during manufacture and rapid apoptosis in the immune microenvironment upon vaccination. This is the principal mechanism of efficacy of the UVC, and fortunately its most redeeming safety feature, by virtue of the impossibility of in vivo persistence and teratogenicity of the cellular antigen carrier. The irradiation-induced apoptosis is further enhanced by CRISPR genetic engineering to remove MHC-I expression and introduce cell surface expression of the NKG2D ligand MICA, making the UVC potent targets for host NK cells. Recruited NK cells will likely recognize the UVC as virally infected cell through ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.27.474288: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a protocol registration statement.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.26.21268358: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

This study has some limitations. The number of participants was limited, and all participants were HCWs vaccinated at a single hospital. Multicenter studies with a larger sample size are needed. In individuals with low antibody response to other viral vaccines, the mechanism by which humoral immunity is acquired after mRNA vaccination needs to be clarified through future research. In conclusion, after two doses of the BNT162b2 vaccine, both low and normal responders to previous antiviral vaccines developed adequate levels of SARS-CoV-2 anti-spike and SARS-CoV-2 neutralizing antibodies to protect against SARS-CoV-2. However, both low and normal responders had lower SARS-CoV-2 anti-spike antibody levels in the fifth month than in the first month after receiving the second dose of BNT162b2 vaccine. Therefore, a third dose of BNT162b2 vaccine should be administered to all individuals, regardless of their antibody response to previous antiviral vaccines.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.27.474251: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.26.474192: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.26.21268380: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.28.474244: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your data.

Our study had several limitations. These included the absence of characterization of cross-neutralizing antibodies in vaccinated mice against the B.1.1.529 Omicron variant, which emerged during the writing of this manuscript. However, we could expect that our vaccine would elicit T-cell responses against N epitopes because of the high homology (100%) between vaccine sequences and this VOC. Due to the limited availability of hCD40/K18-hACE2 mice, we did not evaluate various VOC challenges in mice. Finally we favored the analysis of T cell responses using samples from recovered individuals instead of in vivo preclinical models. Although these responses may be dependent on the “clinical history” of patients and their HLA haplotypes, they are less biased than those that would be observed in an animal model. Our results show that the in-vitro vaccine responses are directed against all vaccine proteins, which confirmed the broad HLA coverage of the vaccine sequences. In conclusion, it is becoming urgent to develop a “pan-sarbecovirus vaccine”. The development of a new protein-based vaccine with expected improved tolerability suitable for people with specific vulnerabilities and children would extend the portfolio of current vaccines and be instrumental in controlling the circulation of the virus and the emergence of new variants. By selecting a narrow range of immunodominant epitopes, presented by a wide variety of HLA alleles and less prone to genetic variations across sarbecoviru...

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04842682</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Dose Escalation Trial of CD40.HIVRI.Env Vaccine Combined or …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04262921</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">French COVID Cohort</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.28.474359: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: Thank you for sharing your code and data.

As already pointed out by DiPiazza et al, drawing conclusions from animal models and extending these observations to the immunological situation in humans may be a difficult task (DiPiazza et al., 2021), considering the limitations of the system, especially in the absence of experience with vaccines targeting SARS-CoV and MERS-CoV and evidence for VAERD of all vaccine concepts including whole-inactivated viruses in humans. However, we were able to replicate VAERD induced by a protein based COVID-19 vaccine candidate with a very similar phenotype in a second animal model, Syrian hamsters, using an unmodified low-passage virus isolate. Therefore, our data strongly support the idea to monitor vaccinated human patients that experience a break-through infection closely. In any case, while our experimental vaccines mimic, but are not the same as the authorized vaccines, these and previously published data by diPiazza et al. point at considerably few concerns for vaccines developed to trigger TH1-biased responses such as viral vector platform-based vaccines and mRNA vaccines. Moreover, even if VAERD as observed in our model should occur in human patients, this immunopathology would be treatable by dexamethasone, which revealed to be an effective medication for severe courses of COVID-19, anyway (Tomazini et al., 2020; Horby et al., 2021). This would be good news also for putative VAERD being mistakenly diagnosed as a variant of the usual forms of severe COVID-19 in a naïve patient. ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

l púlsar binario PSR J0737 como banco de pruebas de la relatividad general Por Francisco R. Villatoro, el 16 diciembre, 2021. Categoría(s): Astronomía • Ciencia • Física • Noticias • Physics • Relatividad • Science ✎ 3

Hulse y Taylor recibieron el Premio Nobel de Física en 1993 por su estudio del púlsar binario PSR B1913+16 (el primero que se descubrió en 1974), que observó de forma indirecta la emisión de ondas gravitacionales. Se publica en Physical Review X un análisis similar del púlsar binario PSR J0737−3039A/B, descubierto en 2003. El púlsar binario PSR J0737 es un banco de pruebas único para el estudio de la relatividad general ya que está situado a solo dos mil años luz de la Tierra, ambas estrellas de neutrones se observan como púlsares y su inclinación orbital es muy próxima a 90 °, luego se puede observar cómo el espaciotiempo curvo del plano orbital modifica los pulsos emitidos. Las observaciones durante 16 años de la precesión del periastro siguen la fórmula de la emisión gravitacional cuadripolar de Einstein con un error menor del 0.013 % (el resultado obtenido tras 2.5 años de observaciones tenía un error del 0.05 % y se publicó en 2006 en Science). Sin lugar a dudas un púlsar binario que habrá que seguir durante las próximas décadas para mejorar estas estimaciones.

Además de probar la fórmula cuadripolar de Einstein, se ha probado el retraso debido al efecto de Shapiro (en un espaciotiempo curvo las señales de radio viajan durante más tiempo y las observamos retrasadas). También se han realizado otras pruebas de la relatividad que hasta ahora no se habían podido realizar con otros púlsares binarios. Por ejemplo, se ha medido la deformación relativista de la órbita (debido al acoplamiento relativista entre el espín (rotación de las estrellas de neutrones) y el momento angular de su órbita). En estas pruebas los resultados tienen mucha mayor incertidumbre, pero en todos los casos son compatibles con las predicciones de la relatividad general de Einstein. Esta teoría, a la que muchos físicos quieren matar cuanto antes, además de muy bella es muy robusta y promete reinar en la física durante muchas décadas.

El artículo es M. Kramer, I. H. Stairs, …, G. Theureau, «Strong-field Gravity Tests with the Double Pulsar,» Physical Review X 11: 04150 (13 Dec 2021), doi: https://doi.org/10.1103/PhysRevX.11.041050, arXiv:2112.06795[astro-ph.HE] (13 Dec 2021); más información divulgativa en Lijing Shao, «General Relativity Withstands Double Pulsar’s Scrutiny,» Physics 14: 173 (13 Dec 2021) [web].

Una manera de destacar la excepcionalidad del púlsar binario PSR J0737 es compararlo con el famoso PSR B1913, que ha sido estudiado durante 35 años. Esta figura muestra la precesión del periastro de la órbita; la diferencia en la densidad de puntos entre 0 y −20 es notable. Así se explica que el nuevo resultado para PSR J0737 tras 16 años tenga un error menor del 0.013 %, cuando para PSR B1913 solo se alcanzó el 0.2 %; por cierto, para las fusiones de agujeros negros observadas por LIGO-Virgo el error típico ronda el 20 %. No le he dicho, pero supongo que sabrás que el periastro de una órbita elíptica es el punto donde la distancia entre ambos cuerpos es mínima; se llama perihelio cuando uno de los cuerpos es el Sol y perigeo cuando es la Tierra. El fenómeno que mide esta figura es análogo a la precesión del perihelio de la órbita de Mercurio, que Einstein usó como guía hacia la formulación correcta de su teoría de la gravitación.

ASTROFÍSICACIENCIAEXPERIMENTOFÍSICANOTICIASPÚLSARTEORÍA DE LA RELATIVIDAD GENERAL

3 Comentarios Mario dice: 17 diciembre, 2021 a las 5:10 pm Francis Hay una frase que no entiendo, favor revisar: «…,luego sus señales se observa cómo el espaciotiempo curvo del plano orbital modificada la señal que observamos». Atte Mario

RESPONDER Francisco R. Villatoro dice: 17 diciembre, 2021 a las 9:15 pm Gracias, Mario.

RESPONDER Mario dice: 19 diciembre, 2021 a las 10:07 pm Francis, entiendo que por el efecto shapiro las señales de radio se ven retrasadas; pero para notar tal retraso tiene que haber una referencia. Cuál es esa referencia?

RESPONDER Deja un comentario

SciScore for 10.1101/2021.12.24.474084: (What is this?)

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Table 1: Rigor

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Results from OddPub: Thank you for sharing your data.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

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SciScore for 10.1101/2021.12.24.474081: (What is this?)

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Table 1: Rigor

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.23.21268005: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

There are some limitations to our findings. First, our sample was a small retrospective analysis of patients with COVID-19 requiring hospitalization. Second, within this cohort of patients, a significant proportion (approximately 20%)did not have blood troponin levelsmeasured and were excluded from the analysis. Furthermore, there were differences in timing of sampling of blood troponin between patients during their hospital stay.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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Results from scite Reference Check: We found no unreliable references.

About SciScore

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SciScore for 10.1101/2021.12.22.473478: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.21.473594: (What is this?)

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Results from OddPub: Thank you for sharing your data.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.20.473447: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.21.473668: (What is this?)

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Results from OddPub: Thank you for sharing your code and data.

Another limitation is our focus on intravenous delivery, whereas intratracheal or inhalation delivery may be more readily applied in patients, especially in the outpatient setting. It would be useful in future studies to use varying doses and delivery route combinations for defined disease stages to identify the optimal combination prior to initiating human efficacy trials. Finally, we chose to fuse the ACE2 peptide to an unmodified Fc from IgG1 (isoallotype nG1m1), whereas others have considered fusions to Fc mutants or IgG4 to dampen interactions with FcγR subtypes that might contribute to inflammation24, 68. We instead reasoned that IgG1 effector functions will be necessary for optimum in vivo protection. In summary, we show for the first time that an engineered decoy ACE2 peptide demonstrating much higher affinity for the SARS-CoV-2 Spike protein is efficacious in vivo against multiple SARS-CoV-2 variants. This peptide prevented viral entry into cells and the peptide’s efficacy against a variant of concern prevented lung endothelial injury and ARDS and significantly reduced mortality. The results show the potential of this engineered peptide to treat COVID-19 patients and others with inadequate antibody titer to protect against emerging, more virulent SARS-CoV-2 variants.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.21.473774: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.20.21268134: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.16.473063: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

A potential limitation of these mouse adapted SARS-CoV-2 viruses is deletion of the QTQTN furin cleavage site flanking sequence, which impairs S1/S2 cleavage by furin (47). Prior S1/S2 cleavage is required for S2’ cleavage by transmembrane protease serine 2 (TMPRSS2) at the cell surface, which is important for entry in TMPRSS2 positive cells. The QTQTN deletion commonly arises after virus propagation in TMPRSS2 negative cell lines (such as Vero E6 and HEK293T), although this deletion is also evident in some human clinical samples (47). This deletion improves cleavage by Cathepsin L, which substitutes for TMPRSS2 by cleaving S2’ in endosomes and releasing viral RNA into the cytoplasm (48). Other studies have shown that deletion of the furin cleavage site attenuates replication in hamsters and K18-hACE mice (49) and reduces transmission in ferrets (50). Our data suggests that this deletion didn’t dramatically affect mouse adapted virus replication or tropism in C57BL/6J mouse lungs compared to other studies (11), although side-by-side comparison with virus containing the same spike amino acid changes as MA1 and MA2 but maintaining furin cleavage would be needed to determine if there is any attenuation. The D614G change, which is present in all SARS-CoV-2 variants (except the ancestral Wuhan strain), also increases virus stability and entry via the cathepsin L route (48). Cathepsin L is widely expressed in human nasal and lung epithelial cells (48), thus our mouse adapted viruse...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.18.473309: (What is this?)

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Table 1: Rigor

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.20.473401: (What is this?)

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Table 1: Rigor

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.16.472155: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr style="background-color:#FF0000"><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT0427541464</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Trial number did not resolve on clinicaltrials.gov. Is the number correct?</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td></tr></table>

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.17.473223: (What is this?)

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Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.15.472838: (What is this?)

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Table 1: Rigor

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Results from OddPub: Thank you for sharing your data.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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Reply to the reviewers

1. General Statements

We thank the reviewers for their helpful comments. We believe that we will be able to address all of their concerns and suggestions. We have highlighted our responses in the revision plan and the changes we have already made to the manuscript in blue text. For figures where we have added data or analyses at the request of reviewers, we have highlighted the corresponding text in the figure legends.

2. Description of the planned revisions

Reviewer #1

2- In Figure 4, the two mutations appear to have statistically differential effects on Rab5 and Rab7 puncta even though the data mean and distribution seem very similar. Interestingly, in each case the non-significant effect is associated with a smaller sample size. Given that the overall sample sizes used are rather small for such highly variable data, this could easily cause a statistical anomaly due to sampling bias. The sample size should be made uniform across all genotypes and should ideally be at least doubled.

We will repeat this staining to increase the n to at least double this number, and adjust our conclusions if need be, in the revised manuscript..

3- Perhaps the most important issue related to Figure 6 where the authors find that there is no sterol accumulation at 96h APF in the Vps50 mutant. However, even that the dendritic phenotype is slower to appear in this mutant compared to the Vps54, are the authors sure that the accumulation is not just slower? This should be examined using the same temporal sequence used for Vps54 shown in Future 6 C. In addition, the fact that sterol accumulation returns to normal in the Vps54 mutant at 1 day, supports the notion of a delay phenotype (see point 1 above). These issues should be experimentally addressed to see if the data fully support the initial conclusions, or if the conclusions should be modified to suggest differential contribution of the two complexes to the process being studied and to a developmental delay phenotype.

We had included the filipin staining for Vps50KO/KO at 1 day in Figure S4 A (which did not show a significant difference from control). We did not collect data for this genotype at 72hrs APF because the dendritic length phenotype didn’t appear until later, and so we did not include Vps50KO/KO in the full time-course in Fig 6 C. We will collect additional data so that we can include Vps50KO/KO at all timepoints in this figure in the revised manuscript.

. Reviewer #2

It is stated that loss of VPS50 and VPS54 only causes dendrite morphogenesis defects. However, the corresponding supplemental figure S2c (which is not referenced in the text), is not suited to address this question. Axonal arborization, in particular terminal arbors, are not visible in samples where multiple/all c4da axons are labeled simultaneously (Fig. S2c). Analogous to the dendrite analysis of c4da neurons single cell resolution is essential to examine this in a meaningful way. Likely, however, c4da neurons may not be a good choice to address this question.

We should be able to get single cell resolution of the c4da axon terminals using MARCM. We already have two of the knockout lines recombined with FRTs (Vps53 and Vps54) for this analysis and we will make the third recombinant line so that we can use MARCM for all three lines to examine single-cell axon morphology, as suggested.

Overall, I am concerned whether the data shown here can be generalized. The cd4a neurons are rather extreme cell types due to their very large dendritic compartment. It seems quite possible that many other neurons may not have a comparable sensitivity to the supply of lipids/sterols. This type of question can only be addressed if other types of neurons/dendrites are examined. Are class 2 or class 3 da neurons showing any defects in VPS mutants?

Given that we see the phenotype emerge during the pupal stage, we want to analyze neurons that persist from the larval to adult stages. However, not all of the dendritic arborization neurons survive into adulthood- class I and II persist, while class III die during metamorphosis (Shimono et al., 2009). As we do not have adequate tools to for studying the class II neurons, we will examine dendrite morphology of the class I neurons in larvae and adults in our knockout lines. We would be happy to look at class III neurons at the reviewers request, but our analysis will necessarily be limited to the larval stage.

Reviewer #3

• Some of the experiments include multiple genotypes and so it would be important to show all in all figures. For example, figure 4B,D show four groups but figure 4F, presumably from the same set of animals, shows only three. Addition of the rescue genotype to 4F is particularly important here so should be shown. The same concern is valid for figure 5, where puncta number and area must be available.

The data from Fig. 4 F (using a genetically encoded marker for lysosomes, UAS-spin-RFP) are not from the same samples as Fig. 4 B and D (staining). We did not include the rescue for Fig 4. F because the lysosome marker, the rescue transgenes and the neuronal membrane marker are all on the third chromosome. We will build additional fly stocks so that we can include the rescue in experiments looking at lysosome morphology.

• This concern is amplified by the images in figure 6 of the filipin staining, that are more obviously perinuclear. However, the two sets of images in 6A and 6D, where co-staining with Golgin245 is shown, look very different. Improved images are required and it may be helpful to use supplementary information to show additional examples of the staining.

The images in Fig. 6 A are maximum projections of z stacks while Fig. 6 D shows single confocal planes, making it easier to see the perinuclear Golgi ring. Because other reviewers wanted some additional experiments related to Fig. 6 that we plan to incorporate into this figure in the revised manuscript, we will address this comment in a future revision and include additional images in the supplement.

• For the lipid regulation experiments in figure 7, please use an orthogonal approach to show that the Osbp and fwd RNAi had the expected effects on lipid accumulation.

In addition to sterol, Osbp and fwd both affect levels of PI4P at the Golgi. We have obtained a transgenic PI4P sensor that we can use to show the effect of these manipulations on this lipid as well.

3. Description of the revisions that have already been incorporated in the transferred manuscript

Reviewer #1 While the data presented clearly support a role for GARP in regulating sterol levels to support dendritic growth, they do not inter current for suffice to exclude a role for EARP as important analyses to allow such a clear cut conclusion are either insufficient or missing. If the authors wish to maintain this claim - as suggested by the title of the manuscript - further analyses are essential.

We don’t mean to argue the EARP complex doesn’t contribute to dendrite development at all – we do show it contributes to development in Fig 3, and as we discuss in the text.. We want to argue that the GARP and EARP complexes contribute to dendrite development by distinct mechanisms. Losing the GARP complex inhibits dendrite development by means of sterol accumulation at the TGN, which is what we are trying to highlight with our title. The reduced dendrite growth that we observe in EARP deficient neurons must occur by some other as yet unknown means. We apologize for the confusion and have reworded the title to read “Sterol accumulates at the trans-Golgi in GARP complex deficient neurons during dendrite remodeling.”

1- Figure 3E shows that whereas both Vps50 and Vps54 mutations reduce dendritic complexity, the Vps54 phenotype appears earlier (96h APF). Furthermore, at 7 days dendrites appear to grow again but at a slower rate than controls. This begs the question of whether these mutations are causing a delay rather than a block in the regrowth after pruning and whether the growth will eventually be normal a few days later or whether it will stop at some point.

We have included data for an additional adult timepoint (21 days) in the new Fig. 3 E. We also included graphs in which we show the statistics for each genotype over time (new Fig. S2 D-F), and discuss this analysis in the text (lines 186-195). We have also included a table of the p-values for each comparison in the Supplemental Materials (Table S2). From this analysis, we conclude that there is not a developmental delay in the knockouts, but rather a decrease in growth during the 72-96hrs APF and 1-7 day windows when the control neurons grow. We are unable to draw conclusions about the rate of growth as we analyzed neurons from different samples at each developmental timepoint, and not the same neurons over time.

Reviewer #2

It would be important to know, whether the dendrite morphogenesis defect is indeed a developmental patterning defect or rather a "scaling" defect due to the fact that da neurons increase their size (but not necessarily their projection pattern) during larval maturation.

We have analyzed the larval data for coverage index – neuron area/hemisegment (receptive field) area as defined in (Parrish et al., 2009) to determine if there is a scaling defect at this stage in development. We do not observe a defect in scaling (Fig. S2 C) and discussed in lines 175-182.

Reviewer #3

• The statistical analyses generally look appropriate but it would be critical to clarify what N means in every case. For example in figure 2 the authors state n=8 without clarifying if this is n=8 animals or n=8 neurons. N should always be the number of animals, but then the n of independent cells counted should also be indicated. Typically, one would either pre-average per genotype or use a mixed model that includes N of animals and n of cells (or similar).

For experiments analyzing dendrite morphology, n represents the number of neurons, as we have clarified in our figure legends. As per another reviewer’s request, we will increase the n for the organelle and filipin staining in our planned revision and specify fly and cell number at that time.

• Please add details of how experiments were blinded to genotype

The researcher was blinded to genotype during analysis. We have included that detail in our Methods section (line 566).

• Some of the experiments include multiple genotypes and so it would be important to show all in all figures. For example, figure 4B,D show four groups but figure 4F, presumably from the same set of animals, shows only three. Addition of the rescue genotype to 4F is particularly important here so should be shown. The same concern is valid for figure 5, where puncta number and area must be available.

We address the first portion of this comment in section 2, for additional experiments involving generating new fly lines. We have included data on puncta area, and mean fluorescence intensity for Rab5 and Rab7 in the supplement (Fig S3). We had already included the data on puncta number and area in Fig 5, but we have added the data on mean fluorescence intensity as well.

• Related to figure 5, please provide validation of the staining of the TGN. Typically, one would expect trans Golgi to be close to the nucleus with at least some extended stacks. A Golgin245 knockout would be ideal.

The Golgi in most Drosophila cells is typically found as discrete puncta dispersed throughout the cytosol like what we see in the Golgin245 staining, as opposed to the ribbon “stack of pancake” morphology typically seen near the nucleus in mammalian cells. For reference, please see Figure 6D in (Ye et al., 2007), Figures 2,4,5 in (Rosa-Ferreira et al., 2015), and observations reviewed in (Kondylis and Rabouille, 2009).

The Golgin245 antibody was well characterized in the paper first describing it (Riedel et al., 2016) (colocalization with other Golgi markers, decreased staining with Golgin245 RNAi), but we would be happy to repeat this validation in the c4da neurons at the reviewer’s request. There do not appear to be Golgin245 mutant or KO lines available, so we would also use the Golgin245 RNAi.

• For figures 6F, G please show examples of staining for late endosomes and lysosome with appropriate validation.

Because several of our planned revisions relate to Fig. 6, we will include images for Fig. 6 F and G when we remake this figure to incorporate those planned revisions. To clarify, we used the same reagents to mark late endosomes and lysosomes in both Fig. 4 and Fig. 6. Like the Golgin245 antibody, the Rab7 antibody was developed by the Munro lab and characterized in (Riedel et al., 2016) (partial colocalization with the endosomal marker Hrs and with the lysosomal marker Arl8). Spinster (aka benchwarmer) is a known lysosomal transmembrane protein that colocalizes with Lamp1 (Dermaut et al., 2005; Rong et al., 2011). The fluorescently tagged spin transgenes were developed by the Bellen lab and have been frequently used to mark lysosomes. We would be happy to carry out additional validation experiments at the reviewer’s specification.

• The title of figure 2 is inaccurate, at least if I understand the experiment, as it does not show neuron-specific knockout but instead whole body knockout with neuron rescue. Please rephrase.

Because of the lethality of whole body Vps53KO/KO in adult flies, we analyze MARCM clonal neurons that are Vps53KO/KO in flies that are otherwise heterozygous (Vps53KO/+). To clarify this experiment, we have changed the title of Fig. 2 from “Neuron-specific knockout of Vps53 results in smaller dendritic arbors” to “Vps53KO/KO MARCM clonal neurons have smaller dendritic arbors”.

• Figure 8 needs examples of the TGN and late endosome morphology.

We have included these images in Figure

The order appears different in Fig. 4 B & D because we only included the rescue for the KO that shows a phenotype for each staining. The genotypes included in Fig. 4 B are: +/+, Vps50KO/KO, Vps50KO/KO + rescue, and Vps54KO/KO. The genotypes included in Fig. 4 D are +/+, Vps50KO/KO, Vps54KO/KO, Vps54KO/KO + rescue. We have changed the shading of the bars corresponding to these rescue genotypes throughout the manuscript to make it easier to distinguish the two rescue conditions.

4. Description of analyses that authors prefer not to carry out

References Cited

Dermaut, B., K.K. Norga, A. Kania, P. Verstreken, H. Pan, Y. Zhou, P. Callaerts, and H.J. Bellen. 2005. Aberrant lysosomal carbohydrate storage accompanies endocytic defects and neurodegeneration in Drosophila benchwarmer. Journal of Cell Biology. 170:127–139. doi:10.1083/jcb.200412001.

Kondylis, V., and C. Rabouille. 2009. The Golgi apparatus: Lessons from Drosophila. FEBS Letters. 583:3827–3838. doi:10.1016/j.febslet.2009.09.048.

Parrish, J.Z., P. Xu, C.C. Kim, L.Y. Jan, and Y.N. Jan. 2009. The microRNA bantam Functions in Epithelial Cells to Regulate Scaling Growth of Dendrite Arbors in Drosophila Sensory Neurons. Neuron. 63:788–802. doi:10.1016/j.neuron.2009.08.006.

Riedel, F., A.K. Gillingham, C. Rosa-Ferreira, A. Galindo, and S. Munro. 2016. An antibody toolkit for the study of membrane traffic in Drosophila melanogaster. Biology Open. 5:987–992. doi:10.1242/bio.018937.

Rong, Y., C.K. McPhee, S. Deng, L. Huang, L. Chen, M. Liu, K. Tracy, E.H. Baehrecke, L. Yu, and M.J. Lenardo. 2011. Spinster is required for autophagic lysosome reformation and mTOR reactivation following starvation. Proceedings of the National Academy of Sciences. 108:7826–7831. doi:10.1073/pnas.1013800108.

Rosa-Ferreira, C., C. Christis, I.L. Torres, and S. Munro. 2015. The small G protein Arl5 contributes to endosome-to-Golgi traffic by aiding the recruitment of the GARP complex to the Golgi. Biology Open. 4:474–481. doi:10.1242/bio.201410975.

Shimono, K., A. Fujimoto, T. Tsuyama, M. Yamamoto-Kochi, M. Sato, Y. Hattori, K. Sugimura, T. Usui, K. Kimura, and T. Uemura. 2009. Multidendritic sensory neurons in the adult Drosophila abdomen: origins, dendritic morphology, and segment- and age-dependent programmed cell death. Neural Dev. 4:37. doi:10.1186/1749-8104-4-37.

Ye, B., Y. Zhang, W. Song, S.H. Younger, L.Y. Jan, and Y.N. Jan. 2007. Growing Dendrites and Axons Differ in Their Reliance on the Secretory Pathway. Cell. 130:717–729. doi:10.1016/j.cell.2007.06.032.

SciScore for 10.1101/2021.12.17.21267926: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Limitation: The major limitation of this trial is its single-center design. Due to the inclusion of hospital employees, women are relatively overrepresented and other groups with a higher risk are underrepresented. Especially elderly participants, with an age over 70 years, are not included in this study. It cannot be excluded that there were asymptomatic, undetected SARS-CoV-2 infections among the participants during the 9 months after second vaccination, which may lead to a slight bias in the results. Due to the use of different methods, it was not possible to compare the absolute values of antibody concentrations, T-cell responses or neutralizing antibodies over the follow-up-period. Further evaluations of antibody response after vaccination are needed, to investigate the longitudinal persistence of antibodies and the possible need for further booster vaccinations.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

Prosser, A., Helfer, B., & Streiner, D. L. (2021). Evaluating the number of unvaccinated people needed to exclude to prevent SARS-CoV-2 transmissions (p. 2021.12.08.21267162). https://doi.org/10.1101/2021.12.08.21267162

A city on the southern coast of Sicily - there are massive Greek temples still standing there

SciScore for 10.1101/2021.12.14.472547: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• No funding statement was detected.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

Garcia-Beltran, W. F., Denis, K. J. S., Hoelzemer, A., Lam, E. C., Nitido, A. D., Sheehan, M. L., Berrios, C., Ofoman, O., Chang, C. C., Hauser, B. M., Feldman, J., Gregory, D. J., Poznansky, M. C., Schmidt, A. G., Iafrate, A. J., Naranbhai, V., & Balazs, A. B. (2021). MRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant (p. 2021.12.14.21267755). https://doi.org/10.1101/2021.12.14.21267755

or 'pipe it to ggplotly()'

SciScore for 10.1101/2021.12.12.472286: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Our study has several limitations, including the use of pseudotyped virus and lack of analysis of T cell responses. However, given the important role that antibodies play in immune protection against SARS-CoV-2, our results suggest that preventive and therapeutic approaches have to be adapted for efficient protection against the Omicron variant. While such adaptations are in progress, heterologous or booster immunizations and conventional control measures like face masks and social distancing will help to limit the impact of the Omicron variant on public health.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.12.21267518: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.10.472112: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.10.472151: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources

Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

• Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
• Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
• No protocol registration statement was detected.

Results from scite Reference Check: We found no unreliable references.

About SciScore

SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

SciScore for 10.1101/2021.12.10.472169: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Table 2: Resources