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

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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

Online marketplaces offer a new take on how goods and services can be exchanged. Consumers no longer require an intermediary to connect to producers, as platforms do the matching. It’s always a good idea to have a big picture of solutions that are currently popular on the market. We’ve categorized these solutions to make it easier for you to see the big picture of peer to peer marketplaces

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.

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

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

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.

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...)

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

Max Primbs on Twitter. (n.d.). Twitter. Retrieved September 14, 2020, from https://twitter.com/MaxPrimbs/status/1304516869509066760

Outbreak Science Rapid PREreview • Dashboard. (n.d.). Retrieved September 11, 2020, from https://outbreaksci.prereview.org/dashboard?q=COVID-19&q=Coronavirus&q=SARS-CoV-2

Rapid Reviews COVID-19. (n.d.). Rapid Reviews COVID-19. Retrieved September 11, 2020, from https://rapidreviewscovid19.mitpress.mit.edu/

Marcus, A. A. (2020, September 8). COVID-19 arrived on a meteorite, claims Elsevier book chapter. Retraction Watch. https://retractionwatch.com/2020/09/08/covid-19-arrived-on-a-meteorite-claims-elsevier-book-chapter/

r/BehSciMeta - Comment by u/dawnlxh on ”A completely re-imagined approach to peer review and publishing: PRINCIPIA”. (n.d.). Reddit. Retrieved September 10, 2020, from https://www.reddit.com/r/BehSciMeta/comments/if03sk/a_completely_reimagined_approach_to_peer_review/g4nnuc5

r/BehSciMeta—No appeasement of bad faith actors. (n.d.). Reddit. Retrieved June 2, 2020, from https://www.reddit.com/r/BehSciMeta/comments/gv0y99/no_appeasement_of_bad_faith_actors/

Clements, J. C. (2020). Don’t be a prig in peer review. Nature. https://doi.org/10.1038/d41586-020-02512-0

About | OpenReview. (n.d.). Retrieved May 30, 2020, from https://openreview.net/about

Schalkwyk, M. C. I. van, Hird, T. R., Maani, N., Petticrew, M., & Gilmore, A. B. (2020). The perils of preprints. BMJ, 370. https://doi.org/10.1136/bmj.m3111. https://t.co/qNPLYCeT99?amp=1

Besançon, L., Peiffer-Smadja, N., Segalas, C., Jiang, H., Masuzzo, P., Smout, C., Deforet, M., & Leyrat, C. (2020). Open Science Saves Lives: Lessons from the COVID-19 Pandemic. BioRxiv, 2020.08.13.249847. https://doi.org/10.1101/2020.08.13.249847

Michael Eisen on Twitter: “A core problem in science publishing today is that we have a system where the complex, multidimensional assessment of the rigor, validity, utility, audience and impact of a work that emerges from peer review gets reduced to a single overvalued ‘accept/reject’ decision.” / Twitter. (n.d.). Twitter. Retrieved August 10, 2020, from https://twitter.com/mbeisen/status/1291752487448276992

Esther Choo, MD MPH on Twitter: “Question for Twitter. Why didn’t academia take the lead on Covid information? Why didn’t schools of med & public health across the US band together, put forth their experienced scientists in epidemiology, virology, emergency & critical care, pandemic and disaster response...” / Twitter. (n.d.). Twitter. Retrieved August 10, 2020, from https://twitter.com/choo_ek/status/1291789978716868608

‘OSF: A Project Management Service Built for Research - ROpenSci - Open Tools for Open Science’. Accessed 10 August 2020. https://ropensci.org/blog/2020/08/04/osf/.

Taraborelli, D., Taraborelli, D., & Taraborelli, D. (2020, August 5). How the COVID-19 crisis has prompted a revolution in scientific publishing. Fast Company. https://www.fastcompany.com/90537072/how-the-covid-19-crisis-has-prompted-a-revolution-in-scientific-publishing

Hoekstra, R., & Vazire, S. (2020, July 29). Hoekstra & Vazire (2020), Intellectual humility is central to science. https://doi.org/10.31234/osf.io/edh2s

Eisen, M. B., & Tibshirani, R. (2020, July 20). Opinion | How to Identify Flawed Research Before It Becomes Dangerous. The New York Times. https://www.nytimes.com/2020/07/20/opinion/coronavirus-preprints.html

Dan Quintana on Twitter: “Tomorrow at 1pm CEST I’ll be doing a virtual talk for the Rotterdam R.I.O.T. Science Club (@rdam_riots) on using Twitter for science 🧬 I’ll be covering both the why and the how + I’ll be leaving plenty of time for a Q&A session. Watch here: https://t.co/nXHry9Inyi https://t.co/T6u7lvgAhO” / Twitter. (n.d.). Twitter. Retrieved June 17, 2020, from https://twitter.com/dsquintana/status/1264623289814659072

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Brock. J. (2020). Rapid Registered Reports initiative aims to stop coronavirus researchers following false leads. Nature index

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Clark, J., Glasziou, P., Mar, C. D., Bannach-Brown, A., Stehlik, P., & Scott, A. M. (2020). A full systematic review was completed in 2 weeks using automation tools: A case study. Journal of Clinical Epidemiology, 121, 81–90. https://doi.org/10.1016/j.jclinepi.2020.01.008

Andrew (2020, June 11) bla bla bla PEER REVIEW bla bla bla.. Retrieved from https://statmodeling.stat.columbia.edu/2020/06/11/bla-bla-bla-peer-review-bla-bla-bla/

Peer Review Practices

Guide the reviewer during the review process

Inspection rate Defect rate Defect density

Set few tangible goals. Fix more bugs is not a good example.

Only less than 500 LOC per hour

<400 LOC

Dr Daniel Quintana | Using Twitter for Science | R.I.O.T. Science Club—YouTube. (2020, May 26). https://www.youtube.com/watch?v=pA5Y4cO934I

Mis-allocated scrutiny. (2020, June 24). The 100% CI. http://www.the100.ci/2020/06/24/mis-allocated-scrutiny/

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Peer review should be an honest, but collegial, conversation. (2020). Nature, 582(7812), 314–314. https://doi.org/10.1038/d41586-020-01622-z

Scholarly publishers are working together to maximize efficiency during COVID-19 pandemic. (2020, April 27). OASPA. https://oaspa.org/scholarly-publishers-working-together-during-covid-19-pandemic/

Lindsay, D. S. (2020, May 29). Enhancing Peer Review of Scientific Reports. Psychonomic Society Featured Content. https://featuredcontent.psychonomic.org/enhancing-peer-review-of-scientific-reports/

Holcombe, A. (2020, May 25). As new venues for peer review flower, will journals catch up? Psychonomic Society Featured Content. https://featuredcontent.psychonomic.org/as-new-venues-for-peer-review-flower-will-journals-catch-up/

Farr, C. (2020, May 23). Why scientists are changing their minds and disagreeing during the coronavirus pandemic. CNBC. https://www.cnbc.com/2020/05/23/why-scientists-change-their-mind-and-disagree.html

Knöchelmann, M. (2020, February 25) Open Humanities: Why Open Science in the Humanities is not Enough. Impact of Social Sciences. https://blogs.lse.ac.uk/impactofsocialsciences/2020/02/25/open-humanities-why-open-science-in-the-humanities-is-not-enough/

Science in the time of COVID-19. Nat Hum Behav 4, 327–328 (2020). https://doi.org/10.1038/s41562-020-0879-9

richard horton on Twitter: “David Spiegelhalter said this morning, ‘Peer review has just disappeared from scientific analysis.’ This is complete and utter nonsense. Our editors across 19 Lancet journals do nothing else but peer review. We intensively review all COVID-19 research papers. You know this David.” / Twitter. (n.d.). Twitter. Retrieved June 5, 2020, from https://twitter.com/richardhorton1/status/1263020292932358145

Wang, M., Jiang, W., & Cheng, P. (2020). Mental Health Peer to Peer Support via Social Media practice reference During COVID-19 Pandemics [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/u4pqy

Heathers, J. (2020, May 21). Preprints Aren’t The Problem—WE Are The Problem. Medium. https://medium.com/@jamesheathers/preprints-arent-the-problem-we-are-the-problem-75d29a317625

Daniël Lakens on Twitter

Lewandowsky, S. (2020, June 1). A tale of two island nations: Lessons for crisis knowledge management. Psychonomic Society Featured Content. https://featuredcontent.psychonomic.org/a-tale-of-two-island-nations-lessons-for-crisis-knowledge-management/

Bajak, A., & Howe, J. (2020, May 14). Opinion | A Study Said Covid Wasn’t That Deadly. The Right Seized It. The New York Times. https://www.nytimes.com/2020/05/14/opinion/coronavirus-research-misinformation.html

Ikeda, K., Yamada, Y., & Takahashi, K. (2020). Post-Publication Peer Review for Real [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/sp3j5