Timmy Broderick in Evidence Undermines ‘Rapid Onset Gender Dysphoria’ Claims In Scientific American at 2023-08-24 (accessed:: 2023-08-25 09:26:00)

German academic publishing in Niklas Luhmann's day was dramatically different from the late 20th/early 21st centuries. There was no peer-review and as a result Luhmann didn't have the level of gatekeeping that academics face today which only served to help increase his academic journal publication record. (28:30)

I somewhat disagree - I think this community building is successful precisely because there is a shared interest or goal. It goes hand in hand. If there is no connecting theme or goal, the groups fall apart.

This might be achievable through Holochain application framework. One promising project built on Holochain is Neighbourhoods. Their "Social-Sensemaker Architecture" across "neighbourhoods" is intriguing

stakesinscience

I don't think we're pretending. I know I'm not!

Do your colleagues who read your work, annotate it, and comment on it not count as peer-review?

Am I wasting my time by annotating all of this? :) (I don't think so...)

This is an apropos question. It is also somewhat contingent on what sort of platform the author "owns" to be able to do outreach and drive readers and participation.

A short text "interview" with the authors of three works that posted versions of their books online for an open review via annotation.

These could be added to the example and experience of Kathleen Fitzpatrick.

This is an intriguing off-label use case for Hypothes.is which is within the realm of peer-review use cases.

Dan is essentially using the idea of annotation as engagement within a textbook as a means of proactively improving it. He's mentioned it before in Hypothes.is Social (and Private) Annotation.

Because one can actively see the gaps without readers necessarily being aware of their "review", this may be a far better method than asking for active reviews of materials.

Reviewers are probably not as likely to actively mark sections they don't find engaging. Has anyone done research on this space for better improving texts? Certainly annotation provides a means for helping to do this.

Abysmally sad that this is presented without the context of any of the work over the last century and a half of spaced repetition.

I wonder that this point slipped past the reviewers and isn't at least discussed somewhat narratively here.

Considering campaigns to post journal reviews on preprints. (n.d.). ASAPbio. Retrieved April 29, 2022, from https://asapbio.org/considering-campaigns-to-post-journal-reviews-on-preprints

Learning has been shown to be linked to engagement with peers in social situations over guidance from faculty mentors.

Cross reference: David F. Feldon et al., “Postdocs’ Lab Engagement Predicts Trajectories of PhD Students’ Skill Development,” Proceedings of the National Academy of Sciences 116 (October 2019): 20910–16

Are there areas where this is not the case? Are there areas where this is more the case than not?

Is it our evolution as social animals that has heightened this effect? How could this be shown? (Link this to prior note about social evolution.)

Is it the ability to scaffold out questions and answers and find their way by slowly building up experience with each other that facilitates this effect?

Could this effect be seen in annotating texts as well? If one's annotations become a conversation with the author, is there a learning benefit even when the author can't respond? By trying out writing about one's understanding of a text and seeing where the gaps are and then revisiting the text to fill them in, do we gain this same sort of peer engagement? How can we encourage students to ask questions to the author and/or themselves in the margins? How can we encourage them to further think about and explore these questions? Answer these questions over time?

A key part of the solution is not just writing the annotations down in the first place, but keeping them, reviewing over them, linking them together, revisiting them and slowly providing answers and building solutions for both themselves and, by writing them down, hopefully for others as well.

Mullins, M. (2021, November 1). Opinion: The Problem with Preprints. The Scientist Magazine®. https://www.the-scientist.com/critic-at-large/opinion-the-problem-with-preprints-69309

Blau, W. (2022, February 14). Climate Change: Journalism’s Greatest Challenge. Medium. https://wblau.medium.com/climate-change-journalisms-greatest-challenge-2bb59bfb38b8

News ·, A. M. · C. (2022, January 15). Canadian COVID-19 vaccine study seized on by anti-vaxxers—Highlighting dangers of early research in pandemic | CBC News. CBC. https://www.cbc.ca/news/health/covid-19-vaccine-study-omicron-anti-vaxxers-1.6315890

Peter R. Hansen. (2022, February 3). Weighting, is the answer. The only study to find lockdowns ⬆️mortality is given weight 91.8% = 7390/8030, and then you get -0.2% to be the estimate. To summarize: -0.2% META-STUDY ESTIMATE is based on 91.8% ONE STUDY and 8.2% ALL OTHER STUDIES. https://t.co/j6e7ziPNAI [Tweet]. @ProfPHansen. https://twitter.com/ProfPHansen/status/1489366528956919808

Kimberly Prather, Ph.D. (2022, January 11). This paper is not published..not reviewed...and has serious problems that will hopefully be fixed during the review process. The lead authors know this. See posts by me @linseymarr @jljcolorado . [Tweet]. @kprather88. https://twitter.com/kprather88/status/1481019341625724928

AAI. (2022, January 29). More than seventy peer-reviewed #COVID-19, #SARS, and #MERS @J_Immunol articles are #FreeToRead http://ow.ly/lwTr50Hyu5F #immunology #ReadTheJI https://t.co/7Hi4g8ZySp [Tweet]. @ImmunologyAAI. https://twitter.com/ImmunologyAAI/status/1487425781647216646

Fischer, O., Jeitziner, L., & Wulff, D. U. (2021). Affect in science communication: A data-driven analysis of TED talks. PsyArXiv. https://doi.org/10.31234/osf.io/28yc5

What is P2P (peer-to-peer) and what can you do with it? https://www.itpedia.nl/wp-content/uploads/2018/12/fingerworld.jpg.webp In a sense, Peer to Peer (P2P) networks are the social networks of the Internet. Every peer is equal to the others, and every peer has the same rights and duties as the others. Peers are clients and servers at the same time.

Replicating scientific results is tough—But essential. (2021). Nature, 600(7889), 359–360. https://doi.org/10.1038/d41586-021-03736-4

Huggins, C., Campbell, A., Porteous, D. J., & Altschul, D. M. (2021). Loneliness in Scottish Adolescents Before, During and After the First National UK Lockdown. PsyArXiv. https://doi.org/10.31234/osf.io/epjrg

AIMOS. (2021, November 30). How can we connect #metascience to established #science fields? Find out at this afternoon’s session at #aimos2021 Remco Heesen @fallonmody Felipe Romeo will discuss. Come join us. #OpenScience #OpenData #reproducibility https://t.co/dEW2MkGNpx [Tweet]. @aimos_inc. https://twitter.com/aimos_inc/status/1465485732206850054

SA is also known as Collaborative Annotation in writing studies, as it focuses on peer-to-peer annotation of a shared document.

Did you know that payment solutions for online marketplaces can shape your e-commerce business and its success? Thus, Uber succeeded in its global expansion right after it switched to Braintree.

In early Uber’s scaling, even a dollar-euro currency conversion wasn’t available. Now, with Braintree, it processes mobile payments in 130 currencies in 80+ countries.

Of course, each marketplace faces its own payment challenges. So, you should rely on a payment solution with the features vital right for your e-commerce platform. To identify them, let’s dig deeper into two-sided marketplace payment processing, and analyze the best payment gateways for marketplaces.

I have no problem with publishers making a profit, or with peer reviewers doing their work for free. The problem I have is when there is such an enormous gap between those two positions.

If publishers make billions in profit (and they do), while at the same time reviewers are doing a billion dollars worth of work for free, that seems like a broken system.

I think there are parallels with how users contribute value to social media companies. In both cases, users/reviewers are getting some value in return, but most of the value that's captured goes to the publisher/tech company.

I'd like to see a system where more of the value accrues to the reviewers. This could be in the form of direct payment, although this is probably less preferable because of the challenges of trying to convert the value of different kinds of peer review into a dollar amount.

Another problem with simply paying reviewers is that it retains the status quo; we keep the same system with all of it's faults and redistribute profits. This is an OK option as it at least sees some of the value that normally accrues to publishers moving to reviewers.

I also don’t believe that open access - in it’s current form - is a good option either. There are still enormous costs associated with publishing; the only difference is that those costs are now covered by institutions instead of the reader. The publisher still makes a heart-stopping profit.

A more elegant solution, although more challenging, would be for academics to step away from publishers altogether and start their own journals, on their own terms.

COVID-19 Living Evidence. (2021, November 12). As of 12.11.2021, we have indexed 257,633 publications: 18,674 pre-prints 238,959 peer-reviewed publications Pre-prints: BioRxiv, MedRxiv Peer-reviewed: PubMed, EMBASE, PsycINFO https://t.co/ytOhLG90Pi [Tweet]. @evidencelive. https://twitter.com/evidencelive/status/1459163720450519042

I'd highlighted this from a pull quote earlier, but note that the full context also includes the phrase:

enforced by heavy peer pressure.

Reuters. (2021, October 6). Sweden, Denmark pause Moderna COVID-19 vaccine for younger age groups. Reuters. https://www.reuters.com/business/healthcare-pharmaceuticals/sweden-pauses-use-moderna-covid-vaccine-cites-rare-side-effects-2021-10-06/

User, S. (n.d.). Long Covid Support. Long Covid. Retrieved August 19, 2021, from https://www.longcovid.org/

Sharma, M., Scarr, S., & Kell, K. (n.d.). Speed Science. Reuters. Retrieved August 19, 2021, from https://graphics.reuters.com/CHINA-HEALTH-RESEARCH/0100B5ES3MG/index.html

User acquisition is one of the most important aspects to make your marketplace website successful. When you attract sellers and buyers to your platform, you start making a profit and improve your market presence.

We prepared 7 quick ways to attract vendors to your peer to peer marketplace platform.

CoronaCentral. (n.d.). Retrieved 11 August 2021, from https://coronacentral.ai/

McIntyre, L. (2021). Talking to science deniers and sceptics is not hopeless. Nature, 596(7871), 165–165. https://doi.org/10.1038/d41586-021-02152-y

CBPP?

u/dawnlxh. (2021). Reviewing peer review: does the process need to change, and how?. r/BehSciAsk. Reddit

Antonoyiannakis, M. (2021). Does Publicity in the Science Press Drive Citations? ArXiv:2104.13939 [Physics]. http://arxiv.org/abs/2104.13939

Health Nerd on Twitter. (2020). Twitter. Retrieved 26 February 2021, from https://twitter.com/GidMK/status/1327872397794439168

Heesen, R., & Bright, L. K. (2020). Is Peer Review a Good Idea? The British Journal for the Philosophy of Science, 000–000. https://doi.org/10.1093/bjps/axz029

Tulleken, C. van. (2021). Covid-19: Sputnik vaccine rockets, thanks to Lancet boost. BMJ, 373, n1108. https://doi.org/10.1136/bmj.n1108

Nicola Low #EveryDayCounts #StillFBPE on Twitter. (2020). Twitter. Retrieved 27 February 2021, from https://twitter.com/nicolamlow/status/1336958661151821825

ReconfigBehSci on Twitter. (2020). Twitter. Retrieved 27 February 2021, from https://twitter.com/SciBeh/status/1339855911796543488

Yesilada, M., Holford, D. L., Wulf, M., Hahn, U., Lewandowsky, S., Herzog, S., Radosevic, M., Stuchlý, E., Taylor, K., Ye, S., Saxena, G., & El-Halaby, G. (2021). Who, What, Where: Tracking the development of COVID-19 related PsyArXiv preprints. PsyArXiv. https://doi.org/10.31234/osf.io/evmgs

Soderberg, C. K., Errington, T. M., Schiavone, S. R., Bottesini, J., Thorn, F. S., Vazire, S., Esterling, K. M., & Nosek, B. A. (2021). Initial evidence of research quality of registered reports compared with the standard publishing model. Nature Human Behaviour, 1–8. https://doi.org/10.1038/s41562-021-01142-4

Sallam, M. (2021). COVID-19 Vaccine Hesitancy Worldwide: A Concise Systematic Review of Vaccine Acceptance Rates. Vaccines, 9(2), 160. https://doi.org/10.3390/vaccines9020160

I was honored to interview Remi and Antero (along with other MITP authors) about collaborative community review and how it fit with their traditional peer review experience. The blog post can be found here.

Calster, B. V., Wynants, L., Riley, R. D., Smeden, M. van, & Collins, G. S. (2021). Methodology over metrics: Current scientific standards are a disservice to patients and society. Journal of Clinical Epidemiology, 0(0). https://doi.org/10.1016/j.jclinepi.2021.05.018

But peer reviewers are largely responsible for generating the assertions you talk about in the next paragraph, and which apparently, justify the cost of publishing.

Polack, R. G., Sened, H., Aubé, S., Zhang, A., Joormann, J., & Kober, H. (2021). Connections during Crisis: Adolescents’ social dynamics and mental health during COVID-19. PsyArXiv. https://doi.org/10.31234/osf.io/x94kv

Trovò, B., & Massari, N. (2021). Ants-Review: A Protocol for Incentivized Open Peer-Reviews on Ethereum. ArXiv:2101.09378 [Cs]. http://arxiv.org/abs/2101.09378

Pleskac, T. J., Kyung, E., Chapman, G. B., & Urminsky, O. (2021, April 23). Single- or double-blind review? A field study of system preference, reliability, bias, and validity. https://doi.org/10.31234/osf.io/q2tkw

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

Learn more at Review Commons

Reviewer #1

1. One key citation missing from the current manuscript is from Hwang et al. 2014 (PMID 25288734). This study has already described that the isp-1 mutant strain survives longer during P. aeruginosa infection. This citation also describes that the gene expression profile of isp-1 mutants animals includes a considerable number of pathogen-responsive genes that are similarly induced during infection. While the current manuscript does go into the mechanism of this resistance with more detail, they should amend the language to more appropriately reflect previous work, notably the above reference.

We apologize for the oversight and have added the suggested citation. Hwang et al. show that isp-1 worms have increased resistance to bacterial pathogens that is dependent on HIF-1/HIF1 and AAK- 2/AMPK. In future work, it will be interesting to examine whether HIF-1 and AAK-2 act in concert with, or independently of, ATFS-1 and the p38-mediated innate immune signaling pathway to mediate pathogen resistance and longevity in isp-1 worms. We will add these points to our discussion.

1. The authors suggest that ROS activation of the p38 MAPK pathway is likely not the mechanism that explains the resistance of long-lived mitochondrial mutant animals due to their reduced food intake. However, is ROS production nonetheless involved? Does antioxidant treatment suppress the increased resistance during infection of isp-1 and/or nuo-6 mutant animals?

To address this question, we will treat wild-type, isp-1 and nuo-6 worms with antioxidant and then measure resistance to bacterial pathogens using the P. aeruginosa strain PA14 slow kill assay. For the antioxidant treatment, we will use 10 mM Vitamin C as we have previously shown that this concentration is effective at reducing ROS in isp-1 worms to decrease isp-1 lifespan (Van Raamsdonk and Hekimi 2012, PNAS). Although antioxidant treatment can have pleiotropic effects, if this decreases survival of bacterial pathogen exposure, it will suggest that the elevated ROS production in isp-1 and

nuo-6 worms may contribute to their enhanced bacterial pathogen resistance.

1. (line 278-282): the authors should elaborate on how the p38 MAPK pathway plays a permissive role. It is intriguing that ATFS-1 and ATF-7 are both bZIP transcription factors that could theoretically heterodimerize and that they share common immune gene targets. The authors do indicate that the binding sites for ATFS-1 and ATF-7 are very different and are likely acting distinctly but some speculation would nonetheless strengthen this statement.

While ATFS-1 and ATF-7 were shown to bind to the promoter regions of the same innate immunity genes, the apparent consensus binding sites are different suggesting that they bind to different regions of the promoter. One way in which the p38 MAPK pathway may be playing a permissive role is that ATF- 7 binding and relief from its repressor activity is required for any transcription of p38-mediated innate immunity target genes to occur. This is consistent with our data showing that disruption of nsy-1, sek-1, pmk-1 or atf-7 decreases the expression of innate immunity genes in wild-type worms. In contrast, it may be that the role of ATFS-1 is for enhanced expression of innate immunity genes such that when ATFS-1 is bound to the promoter region, or perhaps enhancer elements, the baseline expression of innate immunity genes that results from the binding of ATF-7 is increased. This idea is supported by our data showing that disruption of atfs-1 does not affect the expression of innate immunity genes in wild- type worms but prevents nuo-6 mutants from having increased expression. We will update our manuscript to include these points.

1. The authors suggest that reduced food consumption of nuo-6 and isp-1 animals may suppress ROS- induced activation of the p38 innate immune pathway. It is intriguing that dietary restriction was previously shown to increase resistance to infection, presumably through p38-independent mechanisms (PMID 30905669). It would be interesting to measure host survival of nuo-6 and isp-1 mutant animals that are dietary-restricted to see if the enhanced survival rates conferred by mitochondrial stress and DR are additive or not.

According to this suggestion, we will compare the bacterial pathogen resistance of wild-type, isp-1 and nuo-6 worms that have undergone dietary restriction to the same strains under ad libitum conditions. This will determine the extent to which their enhancement of pathogen resistance might be additive.

1. Figure 2: It is intriguing that loss of p38 signaling appears to have different effects in nuo-6 versus isp-1 animals. Specifically, loss of p38 signaling in isp-1 mutants renders them more sensitive to infection than wild-type, whereas it generally suppresses survival rates back to wild-type levels in the nuo-6 mutant background. Even within the nuo-6 mutant group, loss of SEK-1 has more dramatic effects on nuo-6 mutant animals than does loss of NSY-1, PMK-1 or ATF-7(gf). This is despite the fact that the nsy-1, sek-1, and pmk-1 alleles that are used in this study are all reported to be null. Can the authors speculate on these differences?

While the isp-1 and nuo-6 mutations both alter mitochondrial function, they affect different components of the electron transport chain. isp-1 mutations affect Complex III (Feng et al. 2001, Dev. Cell), while nuo-6 mutations affect Complex I (Yang and Hekimi 2010, Aging Cell). Although these mutants both have increased lifespan and a similar slowing of physiologic rates, it is not uncommon to observe differences between these mutants. For example, while treatment with the antioxidant NAC completely reverts nuo-6 lifespan to wild-type, it only partially reduces isp-1 lifespan (Yang and Hekimi 2010, PLoS Biology), suggesting that nuo-6 lifespan may be more dependent on ROS than isp-1. We have recently shown that deletion of atfs-1 reduces nuo-6 lifespan, but completely prevents isp-1 worms from developing to adulthood (Wu et al. 2018, BMC Biology), suggesting that isp-1 worms are more dependent on ATFS-1 than nuo-6 worms. Disruption of sek-1 has a greater impact on pathogen resistance than nsy-1 and pmk-1 because SEK-1 is absolutely required for innate immune signaling, while some partial redundancy exists for NSY-1 and PMK-1. We will add these points to our manuscript.

1. One of the main conclusions from this study is that ATFS-1 likely binds directly to innate immune genes that are in common with ATF-7. Since this is such a pivotal finding, the authors should validate some candidate genes from the referenced ChIP seq datasets using ChIP qPCR. Also, are there predicted ATFS-1 binding sites (PMID 25773600) in these promoters?

Our data shows that activation of ATFS-1 increases the expression of innate immunity genes without increasing activation of p38. The simplest explanation for this observation is that ATFS-1 can upregulate the same innate immunity genes as ATF-7. Accordingly, we hypothesized that ATFS-1 and ATF-7 can bind to the same promoter. Fortunately, two previous ChIP-Seq studies, from well-established laboratories who have extensive experience studying ATFS-1 and ATF-7, had already determined which genes are bound by these two transcription factors (Nargund et al. 2015, Molecular Cell; Fletcher et al. 2019, PLoS Genetics). Comparing the results of these two published studies confirmed our hypothesis by demonstrating that the same innate immunity genes are bound by both ATF-7 and ATFS-1 in vivo. In order to provide additional support for the conclusion that ATFS-1 and ATF-7 can bind to the same genes, we will examine the genetic sequence of innate immunity genes that were shown to be bound by both ATFS-1 and ATF-7 in the published ChIP-seq studies to identify predicted binding sites for ATFS-1 and ATF-7, while noting that the ATFS-1-associated sequence is an enriched motif and not an established binding site. If we are able to identify the predicted binding sites for these two transcription factors in the same gene, it will provide further support for the conclusion that these transcription factors can both bind to the same innate immunity genes.

Reviewer #2

1. The authors state that the p38 MAPK PMK-1 is not activated in the long-lived mitochondrial mutants. However, it might be better to state that there is "no enhanced activation" of PMK-1, since they clearly show in nuo-6 and isp-1 mutants the presence of phosphorylated PMK-1 (Fig. 4A), which would indicate an activated form of PMK-1 in these mutants.**

According to this suggestion, we will change the text to indicate that there is no enhanced activation of PMK-1 in nuo-6 and isp-1 worms.

1. Are the food-intake behaviors of all mutants in liquid culture (Fig. 4B-F) the same as their food- intake behaviors on solid agar media, the environment where pathogen resistance was measured?

We previously compared assays measuring food intake on solid agar media versus the liquid culture approach used in the current study to determine which method is the most robust (Wu et al. 2019, Cell Metabolism). While both assays produced similar results, performing the food intake assay on solid agar plates was much more variable as it is challenging to scrape off all of the uneaten bacteria from solid plates in order to measure it. Since the approach of measuring food intake in liquid media produces more consistent and reliable results, we chose to use this assay for the current study. We will update our manuscript to include this justification.

1. Does the p38 pathway single mutant nsy-1 or sek-1 live shorter than wild type on dead E. coli OP50 (Fig. S9) than they do on live OP50 (Fig. 3)? If so, what might that mean? These mutants are also living shorter than wild type on PA14 (Fig. 2), but live as long as wild type on OP50 (Fig. 3). What is in the live OP50 that allows these mutants to live like wild type?

In a previous publication, we found that sek-1 mutants live shorter than wild-type worms, and nsy-1 live slightly shorter than wild-type worms in a lifespan assay performed in liquid medium with dead OP50 bacteria (Wu et al. 2019, Cell Metabolism). In the current study, we performed lifespan assays on solid NGM plates with live OP50 bacteria and observed a wild-type lifespan in sek-1 and nsy-1 worms. Since there are multiple experimental variables that are different between the previous and current study, most notably liquid versus solid media, the lifespan results cannot be directly compared. In the case of measuring survival of these strains on PA14, the simplest explanation is that they are dying sooner because their innate immune signaling pathway is disrupted, and so they are less able to mount an immune response against the pathogenic bacteria. We will update our manuscript to include these points.

At the same time, wouldn't it be simpler to call the multiple antibiotic-treated OP50 as "dead bacteria", instead of "non-proliferating bacteria"? Some of the antibiotics used to treat OP50 are bactericidal and not bacteriostatic.

We previously monitored the OD600 of the antibiotic-treated, cold-treated OP50 that we used in our experiment, and found that there is only a very small decrease in OD600 after 10 days (Moroz et al. 2014, Aging Cell). Since dead bacteria are rapidly broken down leading to a decrease in OD600, this result is consistent with the bacteria being alive but not proliferating. We will include this point in our manuscript.

1. Since nuo-6 and isp-1 do not always behave exactly the same in their dependence on certain genes (e.g., Fig. 2C vs Fig 2D), what happens in isp-1; atfs-1 double mutants? Do these mutants behave in the same manner as nuo-6; atfs-1?

This is an interesting question. Unfortunately, isp-1;atfs-1 mutants arrest during development (Wu et al. 2018, BMC Biology), which is why we only examined the effect of atfs-1 deletion in nuo-6 mutants. We will update the manuscript to note this point.

Regarding nuo-6; atfs-1, why does the double mutant live shorter on PA14 than either single mutant (Fig. 6A)? Is this because atfs-1 is needed to activate the p38 MAPK-dependent and -independent pathways?

It is possible that the nuo-6 mutation makes worms more sensitive to bacterial pathogens, perhaps due to decreased energy production, and that activation of ATFS-1 is required not only to enhance their resistance to pathogens but also to increase their resistance back to wild-type levels. In a previous study, we showed that loss of ATFS-1 slows down the rate of nuclear localization of DAF-16. Thus, loss of atfs-1 may also be decreasing resistance to bacterial pathogens by diminishing the general stress resistance imparted by the DAF-16-mediated stress response pathway. We will update the manuscript to include these points.

In Fig. 7B, the atfs-1(gof) appears to have slightly more phosphorylated p38 compared to wild type, although it is not statistically significant?

While there is a trend towards a very modest increase in phosphorylated p38 in the constitutively-active atfs-1 mutant compared to wild-type, quantification of four biological replicates indicated that the difference is not significant. This result is consistent with the fact that the levels of phosphorylated p38 are not significantly increased in nuo-6 or isp-1 mutants, both of which show activation of ATSF-1. We have provided raw images of all of these Western blots in our supplementals. In addition, we will repeat these Western blots to determine if this difference becomes significant with additional replicates.

In Fig. 6B, the atfs-1 loss-of-function single mutant also increases the expression of Y9C9A.8, but suppresses it in a nuo-6 mutant background? What might that mean?

It is possible that in wild-type animals disruption of atfs-1 causes a compensatory upregulation of specific stress response genes. We have previously shown that deletion of atfs-1 results in upregulation of chaperone genes involved in the cytoplasmic unfolded protein response (hsp-16.11, hsp-16.2; Wu et al. 2018; BMC Biology). Perhaps Y9C9A.8 is acting in a similar way. In nuo-6, the upregulation of Y9C9A.8 is driven by activation of ATFS-1, and thus is prevented by atfs-1 deletion. We will add these points to the manuscript.

Reviewer #3

1. Some studies propose that OP50 offers some toxicity to worms which is not observed in other bacterial strains like HT115. The authors should test the role of the p38-innate immune signaling pathway in nuo-6 and isp-1 lifespan using other non-pathogenic E. coli strains.**

To determine if the effect of disrupting the p38-mediated innate immune signaling pathway on the lifespan of isp-1 and nuo-6 mutants was simply the result of losing protection against OP50 bacteria, we examined the effect of nsy-1, sek-1 and atf-7(gof) mutations on isp-1 and nuo-6 lifespan using non- proliferating bacteria. We found that even when no proliferating bacteria are present, disruption of the p38-mediated innate immune signaling pathway markedly decreases isp-1 and nuo-6 lifespan. This suggests that the p38-mediated innate immune signaling pathway is required for their long lifespan independently of its ability to protect against bacterial infection. Similarly, we have previously shown that lifespan extension resulting from dietary restriction is dependent on the p38-mediated innate immune signaling pathway even when non-proliferating bacteria are used (Wu et al. 2019, Cell Metabolism). We will clarify this important point in the manuscript.

1. The authors should measure food intake in worms exposed to pathogenic bacteria, given that reduced bacterial intake may be related to reduced mortality.

Unfortunately, it is not feasible to perform the food intake assay using the pathogenic bacteria because the bacteria cause death thereby complicating the calculation of food consumed per worm (which requires at least 3 days to assess). As an alternative to measuring food intake, we will attempt to measure intestinal accumulation of P. aeruginosa, which is a balance between food intake and other factors. To do this we will use a P. aeruginosa strain that expresses GFP and quantify the amount of intestinal fluorescence in wild-type, isp-1 and nuo-6 worms that have been grown on the GFP-labelled P. aeruginosa.

1. The authors should check if ROS is required for the activation of the p38-mediated innate immune signaling pathway and reduction in food intake.

To determine if the elevated ROS that is present in isp-1 and nuo-6 worms affects activation of the p38- mediated innate immune signaling pathway, we will treat wild-type, isp-1 and nuo-6 worms with Vitamin C and measure the ratio of phosphorylated p38 to total p38 by Western blotting. Similarly, to examine the effect of ROS on food intake, we will treat wild-type, isp-1 and nuo-6 worms with Vitamin C and then quantify its effect on food intake. For these experiments, we will use 10 mM Vitamin C as we have previously shown that this concentration is effective at reducing ROS in isp-1 worms to decrease isp-1 lifespan (Van Raamsdonk and Hekimi 2012, PNAS).

1. Since ATFS-1 and the p38 pathway control food intake, how related to dietary restriction the phenotypes the authors are studying are?

While the lifespan extension that results from mild impairment of mitochondrial function and the lifespan extension resulting from dietary restriction are both dependent on the p38-mediated innate immune signaling pathway, these interventions modulate innate immunity gene expression in opposite directions. We previously reported that dietary restriction primarily downregulates innate immunity genes (Wu et al. 2019 Cell Metabolism). Here, we show that mutations in isp-1 or nuo-6 primarily result in upregulation of innate immunity genes. To more globally examine gene expression changes between dietary restriction and mild impairment of mitochondrial function, we compared differentially expressed genes. We found that there was very little overlap of either upregulated or downregulated genes between dietary restriction and isp-1/nuo-6 mutants. We will add a supplementary figure to demonstrate this, and add these points to our manuscript.

1. Somewhat related to the previous points, I am not so sure whether the changes in food intake are cause or consequence of the alterations in the innate immunity-related genes. Reduced food intake is depicted in Fig. 8 as the cause of the activation of the p38 pathway, but there is not enough evidence to unequivocally prove that. In fact, food intake might be controlled by the p38 or ATFS-1 pathway or by a common regulator such as ROS.

We apologize that we didn’t make this clearer. In our previous work, we showed that dietary restriction results in decreased activation of the p38 pathway (Wu et al. 2019, Cell Metabolism). Here, we show that activation of ATFS-1 results in decreased food intake. Based on our previous study, this decrease in food intake should similarly decrease p38 pathway activation. In Figure 8, we have depicted ATFS-1 inhibiting food intake, and food intake activating the p38-mediated innate immune signaling pathway. Combined, our model suggests that activation of ATFS-1 should act to decrease p38-mediated innate immune signaling. We will clarify this in the figure legend.

1. I am not so convinced of the role of DAF-16. In fact, in Fig. 5A daf-16 mutation reduces pathogen resistance and that could represent a toxic effect of the mutation. Furthermore, the results in Fig. 4D do not exclude the possibility that daf-16 and isp-1 act in parallel.

We agree that the role of DAF-16 could be non-specific. While we show that disruption of daf-16 leads to decreased bacterial pathogen survival in isp-1 worms, it also decreases bacterial pathogen survival in wild-type worms. Since DAF-16 is known to be required for general resistance to stress, the decreased survival when daf-16 is disrupted could be due to a general toxic effect of reducing general stress resistance. This conclusion is consistent with our observation that DAF-16 is not involved in the upregulation of innate immunity genes in isp-1 worms. We will emphasize these points in our manuscript.

1. Loss of innate immunity related genes may result in toxicity and sensitize worms to pathogenic bacteria. This is further supported by an even lower resistance to pathogens in the double mutants mainly in Fig. 2D.

We agree. Our data confirms that disruption of the p38-mediated innate immune signaling pathway makes worms more susceptible to bacterial pathogens. We will emphasize this point.

1. The blots are saturated, particularly in Fig. 4A, and this can be masking the differences in p38 phosphorylation. In fact, the fact that p38 phosphorylation is not changed is contradictory to the other results. How is p38 regulated by mitochondrial mutations then? I am concerned that p38 is actually not altered and the changes in gene expression are exclusively due to ATFS-1. The interaction with the p38 pathway demonstrated genetically could be due to the toxicity elicited by the loss of function mutations in this pathway.

To address this concern, we will repeat the Western blotting experiment to compare the ratio of phosphorylated p38 to total p38 between wild-type, isp-1 and nuo-6 worms. We will take multiple exposures to ensure that the blots are not over-saturated. Having already completed four replicates, we believe that there is not a major change in p38 activation. Our data suggests that the p38-mediated innate immunity pathway is playing a permissive role such that it is required for baseline expression of innate immunity genes, but that activation of ATFS-1 is driving the enhanced expression of innate immunity genes that we observe in the long-lived mitochondrial mutants and constitutively active atfs-1 mutants. We will update our manuscript to clarify this.

Minor concerns

1. Lines 167 and 174: What are these p values referred to?**

The p-values indicate the significance of the overlap between the two gene sets. Given the size of the two gene sets, this is the probability that the observed number of overlapping genes would result by picking genes at random. We will clarify this in the manuscript.

1. Line 258: I partially agree with the conclusions, since the functions may not necessarily be associated with innate immune signaling but rather other functions of p38.

Since isp-1 and nuo-6 worms have extended longevity even when grown on non-proliferating bacteria this indicates that their long life is not dependent on their enhanced resistance to bacterial pathogens. Similarly, since disruption of genes in the p38-mediated innate immune signaling pathway decrease isp- 1 and nuo-6 lifespan even when the worms are grown on non-proliferating bacteria, this suggests that this pathway enhances longevity independently of its ability to increase innate immunity.

1. Why in figures 4D and E different mutants were used?

We only used isp-1 mutants to examine the effect of daf-16 because we were unable to generate nuo- 6;daf-16 mutants due to close proximity of the two genes on the same chromosome. We only used nuo- 6 mutants to examine the effect of atfs-1 because isp-1;atfs-1 worms arrest during development. We will include this explanation in our manuscript.

1. Line 498: revise writing.

We will rewrite this sentence to improve clarity.

1. Show blots in Fig. 7B.

We will provide an image of a representative Western blot in Figure 7, and will provide the raw images for all of Western blots in our supplementals.

1. It would be interesting to know where the activation of the immune-related genes by the mitochondrial mutations is happening, whether this is a cell autonomous or cell non-autonomous mechanism.

While it would be interesting to explore whether specific tissues are important in sensing mitochondrial impairment in order to upregulate genes involved in innate immunity, it is beyond the scope of this manuscript. Previous work has shown that knocking down the expression of the cytochrome c oxidase gene cco-1 in neurons can activate the ATFS-1 target gene hsp-6 in the intestine (Durieux et al., 2011). Based on this, one could hypothesize that a similar cell non-autonomous mechanism might be involved. We will note this possible future direction in our discussion.

Volle Transparenz wäre m.E. erst dann gegeben, wenn auch abgelehente Einreichungen mitsamt der der Gutachten, die zur Ablehnung geführt haben ins Netz gestellt werden. Mir scheint, um Meinungs- oder Zitationskartelle zu verhindern (oder zumindest offensichtlich werden zu lassen), wäre das sogar wichtiger als die Namen der Gutachter anzugeben.

Machine learning models for diagnosing COVID-19 are not yet suitable for clinical use. (2021, March 15). University of Cambridge. https://www.cam.ac.uk/research/news/machine-learning-models-for-diagnosing-covid-19-are-not-yet-suitable-for-clinical-use

Mambrini, A., Baronchelli, A., Starnini, M., Marinazzo, D., & De Domenico, M. (2020). PRINCIPIA: A Decentralized Peer-Review Ecosystem. ArXiv:2008.09011 [Nlin, Physics:Physics]. http://arxiv.org/abs/2008.09011

Oraby, T., Thampi, V., & Bauch, C. T. (2014). The influence of social norms on the dynamics of vaccinating behaviour for paediatric infectious diseases. Proceedings of the Royal Society B: Biological Sciences, 281(1780). https://doi.org/10.1098/rspb.2013.3172

COVID-19 Living Evidence. (2020, October 23). Weekly update of COAP As of 23.10.2020, we have indexed 80588 publications: 8902 pre-prints 71686 peer-reviewed publications Pre-prints: BioRxiv, MedRxiv Peer-reviewed: PubMed, EMBASE https://t.co/RaDy1Wm4Hq https://t.co/FYRaYPe8oG [Tweet]. @evidencelive. https://twitter.com/evidencelive/status/1319578431848353793

Deevybee. (2020, December 6). BishopBlog: Faux peer-reviewed journals: a threat to research integrity. BishopBlog. http://deevybee.blogspot.com/2020/12/faux-peer-reviewed-journals-threat-to.html

ReconfigBehSci. (2020, November 9). final speaker in our ‘Open science and crisis knowledge management’ session: Michele Starnini on radically redesigning the peer review system #scibeh2020 https://t.co/Gsr66BRGcJ [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1325734449783443461

Collabovid. (n.d.). Retrieved 6 March 2021, from https://www.collabovid.org/

PRINCIPIA - Decentralized peer review. (n.d.). Retrieved 5 March 2021, from http://www.principia.network/

Conference Details. (n.d.). AIMOS. Retrieved 5 March 2021, from https://aimos.community/2020-details

Market, R. T. (n.d.). Build trust through criticism. Red Team Market. Retrieved 4 March 2021, from https://redteammarket.com/

ReconfigBehSci on Twitter. (n.d.). Twitter. Retrieved 1 March 2021, from https://twitter.com/SciBeh/status/1354456391772229632

Dr Elaine Toomey on Twitter. (n.d.). Twitter. Retrieved 24 February 2021, from https://twitter.com/ElaineToomey1/status/1357343820417933316

Chen, Y.-H., Glymour, M., Riley, A., Balmes, J., Duchowny, K., Harrison, R., Matthay, E., & Bibbins-Domingo, K. (2021). Excess mortality associated with the COVID-19 pandemic among Californians 18–65 years of age, by occupational sector and occupation: March through October 2020. MedRxiv, 2021.01.21.21250266. https://doi.org/10.1101/2021.01.21.21250266

This is an untested statement and does not take into account the perspectives of those contributing to the publishers' revenue. The Rights Retention Strategy (RRS) relies on the author's accepted manuscript (AAM) and for an AAM to exist and to have the added value from peer-review a Version of Record (VoR) must exist. Libraries recognise this fundamental principle and continue to subscribe to individual journals of merit and support lucrative deals with publishers. From some (not all) librarians' and possibly funders' perspectives these statements could undermine any mutual respect.

ReconfigBehSci [@SciBeh] (2020-01-27) new post on Scibeh's meta-science reddit describing the new rubric for peer review of preprints aimed at broadening the pool of potential 'reviewers' so that students could provide evaluations as well! https://reddit.com/r/BehSciMeta/comments/l64y1l/reviewing_peer_review_does_the_process_need_to/ please take a look and provide feedback! Twitter. Retrieved from: https://twitter.com/SciBeh/status/1354456393877749763

Mambrini. A. Baronchelli. A. Starnini. M. Marinazzo. D. De Domenico, M. (2020) .PRINCIPIA: a Decentralized Peer-Review Ecosystem. Retrieved from: chrome-extension://bjfhmglciegochdpefhhlphglcehbmek/pdfjs/web/viewer.html?file=https%3A%2F%2Farxiv.org%2Fpdf%2F2008.09011.pdf

Soderberg, C. K., Errington, T., Schiavone, S. R., Bottesini, J. G., Thorn, F. S., Vazire, S., Esterling, K. M., & Nosek, B. A. (2020). Research Quality of Registered Reports Compared to the Traditional Publishing Model. MetaArXiv. https://doi.org/10.31222/osf.io/7x9vy

An in depth read that has plenty of sources and data to back its findings that peer evaluation has many positive impacts on learning when done the correct way.

8/10

Health Nerd on Twitter. (n.d.). Twitter. Retrieved October 17, 2020, from https://twitter.com/GidMK/status/1316511734115385344

Definitely something the IndieWeb may have to solve for.

Daniël Lakens on Twitter. (n.d.). Twitter. Retrieved September 23, 2020, from https://twitter.com/lakens/status/1308115862247952386