"If you want to be one year behind, don’t read bioRxiv” – Jeff LeekWelcome to PREreview! On PREreview you can collaboratively write reviews of preprints. This project was born in April 2017 as a collaboration eetween Samantha Hindle and Daniela Saderi, scientists and ASAPbio Ambassadors, with help from Josh Nicholson, at the time working for Authorea. ASAPbio (Accelerating Science And Publication in biology) is a non-profit organization dedicated to spreading the word about preprints to accelerate scientific discovery.As of October 2018, we are proud to have become an official project fiscally sponsored by Code for Science and Society. Learn more in this blog post.We are also proud to announce that we have received funding from the Sloan Foundation and the Wellcome Trust to continue to grow our community. Reed more here and stay tuned for some exciting updates! Our Mission PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to collaboratively review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation.
We are proud to introduce you to the members of our Advisory Committee. These fantastic people have been unofficially supporting us throughout the launch of PREreview, and we are honored that they have agreed to continue their support in a more official fashion. We look forward to building and improving PREreview together.
Our PledgeIn the interest of fostering an open and welcoming environment we, as contributors and maintainers, pledge to making participation to this project and community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.We believe it is our duty as scientists at any level of our career to contribute to scientific evaluation in the form of peer review. PREreview provides a space for any researcher, independently of their career level, to provide feedback to emerging scientific output. We strive to build and support a community of PREreviewers who provide constructive feedback, because we are convinced that one can be honest AND respectful at the same time.
At the top write: Title of the preprint, authors, date of submission, version number, preprint server, and digital object identifier (DOI)Start a new document and invite to your preprint journal club others who want to collaboratively write the preprint review – they will have to sign up on PREreview to be able to edit. Below are a short list of questions that you can have journal club attendants answer (PREreview short participant worksheet, example here), followed by more detailed guidelines on how to structure a more formal and complete peer review (PREreview peer review, example here). Answering the first set of questions will be faster and still povide useful feedback to the authors. However, if the main purpose of the preprint journal club is to train early-career researchers on how to write a peer review, recommend you write the full review as if you were a reviewer for a journal. You can use the comments from the first one to construct the preprint peer review. After you are done writing your your PREreview, you can click on "Document" (top left), "Publish" so that your preprint review will be public and will be assigned a DOI that you can use to advertise your review on social media, email to the authors, and post on the comment section on the server that hosts the preprint you chose for your JC. Additionally with a DOI, your preprint review will be citable! If you got this far, GREAT JOB! Thank you for supporting open science and helping science move forward faster!
Where you can find preprints:There are various preprint repositories (see below) and also website platforms where you can search all/most of the preprint repositories, including Prepubmed, Publons, The Winnower, and Academic Karma (please let us know at firstname.lastname@example.org or leave a comment on this page if we missed any). You can search the Research Preprint Servers List to find a preprint server in your field.Below is a list of the most common preprint repositories that post findings in the biological sciences:AgriXiv: a preprint repository for agriculture and allied sciencesarXiv q-bio: a preprint repository for quantitative biology operated by the Cornell University Library. This repository includes manuscripts in the following categories: Biomolecules, Cell Behavior, Genomics, Molecular Networks, Neurons and Cognition, Subcellular Processes, Populations and Evolution, Tissues and Organs, Quantitative Methods, and Other Quantitative BiologybioRxiv: a preprint repository for the biological sciences operated by Cold Spring Harbor Laboratory. This repository includes manuscripts in the following areas: Animal behavior and Cognition, Biochemistry, Bioengineering, Bioinformatics, Biophysics, Cancer Biology, Cell Biology, Clinical Trials, Developmental Biology. Ecology, Epidemiology, Evolutionary Biology, Genetics, Genomics, Immunology, Microbiology, Molecular Biology, Neuroscience, Paleontology, Pathology, Pharmacology and Toxicology, Physiology, Plant Biology, Scientific Communication and Education, Synthetic Biology, Systems Biology, and ZoologyOSF PREPRINTS: a preprint server that hosts preprints from a broad range of disciplines, including the Life Sciences, and Medicine and Health Sciences PeerJ Preprints: a preprint repository for the biology and computer sciencesPreprints.org: a preprint repository that posts manuscripts covering many areas of the biology and biomedical science (and other sciences, arts and humanities), including Behavioral Sciences, Biology, Life Sciences, and Medicine and PharmacologyWellcome Open Research: a preprint repository for research funded by the Wellcome Trust mainly in areas of the biological sciences, population health, applied research, humanities and social scienceINARxiv: the preprint server for Indonesia powered by OSF Preprints hosting preprints from a broad range of disciplines, including the Life Sciences, and Medicine and Health SciencesEarthArXiv: the preprint server for Earth Sciences powered by OSF Preprints
What are preprints?Preprints are complete pieces of scientific work that have not yet undergone editorial peer reviewed. Preprints are often the same manuscripts that are submitted to a journal for peer review, but are stored on freely accessible public servers (repositories) such that they become available to the whole web community within 1-2 days from submission. Usually preprints are posted on preprint repositories (see below) either before or at the same time as submission to a journal. Most journals will accept manuscripts that have previously been submitted to a preprint repository. A list of copyright and self-archiving polices can be found on Wikipedia and SHERPA/RoMEO.
In the summer of 2017, we conducted a survey to assess scientists' opinions on the value and potential barriers related to reading and reviewing preprints at journal clubs. In this short article we present and discuss the results of the survey as well as how these results helped us shape our approach at PREreview.
REQUEST A LIVE-STREAMED PREreview JOURNAL CLUBAt PREreview, we want to take preprint journal clubs to the next level. Live-streamed PREreview journal clubs (LivePREJCs) are hosted via online community calls, allowing anyone with internet or phone-in capabilities to join the discussion. This format promotes inclusivity by following a structure that provides a means to join the discussion silently in written form and vocally. You can request our help to organize a live-streamed preprint journal club by clicking on the link above and filling the form. Here is a list of current and past LivePREJCs.Live-streamed PREreview journal clubs are:Inclusive: anyone, anywhere in the world with a internet or phone connection can joinInformative: you can learn more about the topic by listening to/reading the comments of other researchers in the field and even the authors themselves (if invited)Efficient: if preprint authors are present, they receive feedback in real time. Also, we restrict the live journal clubs to 1 hour to keep the feedback focused and efficientCollaborative: the format encourages contributions from all participants regardless of input style preference, i.e. both vocal and silent writing (etherpadding)Fun: even though the discussions are kept professional and centered around providing constructive feedback to the preprint authors, they are a fun way to meet other people interested in the field.How to get started:Choose a preprint you wish to discuss at a LivePREJC (find out more about what preprints are and where to find them).Find a few other scientists or researchers, preferably at different career levels and from different institutions, who would like to participate in the LivePREJC. Our team will help you recruit more participants if you cannot find them on your own.Fill out this form to formally request a LivePREJC and our logistic support.If you are not the preprint author(s), you can contact the corresponding author(s) and let them know about the LivePREJC. If you don't feel comfortable doing this, please let us know and we will do it on your behalf. You can also choose not to include the author(s) in the discussion. What to expect during the call:LivePREJCs are usually hosted by one or two members of the PREreview team: we will ensure that the conversation around the preprint runs smoothly and stays on time (1 hour); they will take notes and encourage others to take notes on a collaborative etherpad (see below); importantly, they will set the tone for a productive and respectful conversation according to the PREreview code-of-conduct.Preprint authors interested in having their preprint discussed on a LivePREJC, will have the option to be present (recommended). We advise authors to find 5-10 participants (not all the participants need to be experts in the field). Our team will help coordinate the call and, if the authors request it, help recruit more researchers in the field by advertising the call on social media using the #LivePREJC hashtag and any other hashtag related to the research field of the preprint discussed.Once the preprint authors have identified the participants, we will send out a short email with instructions on how to join the LivePREJC and with a copy of the preprint. Participants will be encouraged to read the preprint before the LivePREJC, to keep the discussion short and focused.Authors will be asked to remain in ‘listening mode’ – except when asked a question by participants - until the last 10 minutes reserved for this discussion. This will encourage participants to express their constructive feedback freely and stimulate a productive discussion.Participants will be given the opportunity to give feedback both vocally (with notes taken by one of the PREreview team) and in written form (via collaborative note-taking on a public etherpad that we will set up for each LivePREJC). Here is an example of an etherpad template that will be used for the LivePREJCs.
The following guidelines and email templates are meant to help you start a PREreview journal club at your institution. The first two email templates are for you to send to your department to invite colleagues to your journal club; the last one is for you to send to the authors to let them know you have reviewed their preprint on PREreview. Please let us know if these materials helped you, or suggest changes by emailing us at email@example.com. Thank you!
Dustin Revell and Zhang Li“Notch signaling regulates Akap12 expression and primary cilia length during renal tubule morphogenesis” Preprint posted to BioArchiv on September 9, 2019; doi: https://doi.org/10.1101/760181This preprint was reviewed as part of the Developmental Biology Journal Club at the University of Alabama Birmingham and the review is a summary of the group discussion.Mukherjee et al. used a combination of transgenic inducible mouse models as well as cell culture and spheroid models to demonstrate how Notch signaling regulates Akap12 expression to influence primary cilia length during renal tubule morphogenesis. The authors show that inhibition of Notch signaling through expression of dnMaml or the conditional deletion of RBPJ leads to kidney cysts and elongated cilia, mimicking the human disease Alagile syndrome. While these data are very interesting and lean towards the classification of Alagile syndrome as being one of the class of diseases termed ciliopathies , we found several concerns throughout the paper which are outlined below.Major Concerns:1) There is some confusion in the use of the different transgenic mouse models used in the paper. For Figures 1 and 2, the authors utilize the Pax8-rtTA; TRE-dnMamL model which will express dnMamL in the kidney of mice when treated with doxycycline. However, in Figure 5, the authors switch to a Rarb2-Cre; RBPJ(flox/flox) mouse without any introduction or explanation as to why. As Rarb2 is expressed in multiple tissues, not just the kidney, this may be influencing their results (https://www.ncbi.nlm.nih.gov/gene/5915).2) We feel that there should be some further validation to show that Notch signaling is truly reduced and in which cell types upon use of the Pax8-rtTA; TRE-dnMamL - This could be done via qRT-PCR looking at the common downstream genes HES and HEY. It is previously published that complete inhibition of Notch2 results in a lack of proximal tubules in murine kidney resulting in death at P0 (Kamath, Spinner, & Rosenblum, 2013; McCright et al., 2001). Figure 1D shows a large reduction in LTA positive proximal tubules suggesting that dnMamL might be causing an incomplete inhibition of Notch resulting in the renal phenotype.3) We are concerned as to the variability in the length of the primary cilia between cell culture experiments. In Figure 4C, the WT MDCK primary cilia were an average length of approximately 1.5microns, while in Figure7H, the WT cilia were less than 500nm in length. Primary cilia are generally between 3 to 5 microns in length (Keeling, Tsiokas, & Maskey, 2016), so this discrepancy leads to skepticism over the health of these MDCK cells and the conclusions made from these experiments.4) The authors conclude that inhibition of Notch signaling regulates Akap12 expression to increase cilia length during tubule morphogenesis. While the authors do show a clear demonstration that Akap12 is upregulated in the dnMamL MDCK cells and in E16.5-18.5 embryos from the Pax8-rtTA; TRE-dnMamL line, and that ectopic expression of Akap12 in MDCK cells is sufficient to increase cilia length, they do not provide conclusive evidence of the link between Notch and Akap12, the link between elongated cilia and cyst formation, or provide conclusive evidence that Akap12 overexpression induced cilia elongation is causal to cyst formation in vivo . In the discussion, the authors bring up a possible role of Akap12 to bind AuroraA and Plk1 to regulate spindle orientation, but fail to mention that AurA and Plk1 arethe major deciliogenesis pathways (Pugacheva, Jablonski, Hartman, Henske, & Golemis, 2007; Sanchez & Dynlacht, 2016) , and Akap12 overexpression could result in increased cilia length simply because AurA and Plk1 are no longer able to activate HDAC6 to reduce cilia length. In addition, Akap12 is also known to bind kinases such as PKA, which also is known to play a key role in cilia length maintenance through IFT protein phosphorylation (Abdul-Majeed, Moloney, & Nauli, 2012).Minor Concerns:1) In Figure 2, we wonder why A-D are H&E staining, while E-F are immunofluorescence. In addition, we wonder why the authors now stain for Megalin instead of LTL to detect proximal tubule segments.2) We think that the data presented in Figure 1 and Figure 2 would be strengthened by the addition of quantification of kidney size or cystic index, especially comparing the severity of the different induction timepoints of Figure 2.3) In Figure 3C, we are unsure what the X-axis labels (D2, B2, F3, A2, F2) are. Please clarify.4) In Figure 6, we are unsure what conclusion the authors are trying to draw. For instance, in the text they refer to a more “motile-like cilia phenotype”, yet Figure 6D, G, and H show 8 microtubule doublets with a misplaced doublet in the center, which happens in normal primary cilia as you image more distally from the cell body. They also lack the electron dense NDRC components and dynein arms which are present in motile cilia. To say whether or not the ciliary ultrastructure is disrupted, the authors would need to do 3D reconstruction using a technique such as scanning block face EM to ensure you are in the same region when comparing cilia.Abdul-Majeed, S., Moloney, B. C., & Nauli, S. M. (2012). Mechanisms regulating cilia growth and cilia function in endothelial cells.Cell Mol Life Sci, 69 (1), 165-173. doi:10.1007/s00018-011-0744-0Kamath, B. M., Spinner, N. B., & Rosenblum, N. D. (2013). Renal involvement and the role of Notch signalling in Alagille syndrome.Nat Rev Nephrol, 9 (7), 409-418. doi:10.1038/nrneph.2013.102Keeling, J., Tsiokas, L., & Maskey, D. (2016). Cellular Mechanisms of Ciliary Length Control. Cells, 5 (1). doi:10.3390/cells5010006McCright, B., Gao, X., Shen, L., Lozier, J., Lan, Y., Maguire, M., . . . Gridley, T. (2001). Defects in development of the kidney, heart and eye vasculature in mice homozygous for a hypomorphic Notch2 mutation.Development, 128 (4), 491-502.Pugacheva, E. N., Jablonski, S. A., Hartman, T. R., Henske, E. P., & Golemis, E. A. (2007). HEF1-dependent Aurora A activation induces disassembly of the primary cilium. Cell, 129 (7), 1351-1363. doi:10.1016/j.cell.2007.04.035Sanchez, I., & Dynlacht, B. D. (2016). Cilium assembly and disassembly.Nat Cell Biol, 18 (7), 711-717. doi:10.1038/ncb3370
This is a preprint journal club review of "Age-related decline in behavioral discrimination of amplitude modulation frequencies compared to envelope-following responses" by Jesyn Lay, Edward L. Bartlett. The preprint was posted on bioRxiv on Sep 28, 2017 (DOI: http://dx.doi.org/10.1101/193268).Our group reviewed this paper on October 13, 2017 and used the PREreview quick participant worksheet.
This is a review of Baudin, Schreiber, Martin et al. bioRxiv doi: https://doi.org/10.1101/592824 posted on March 29, 2019. The authors used structural modelling to identify elements required for self-association of the NLR immune receptor ZAR1, specifically its N-terminal CC-domain ZAR1CC. They discovered that the N-terminal α1 helix and EDVID motif in ZAR1CC are important for oligomerization and function of ZAR1. This complements recent findings by Wang et al. (2019) based on cryo-EM structures, highlighting the importance of the α1 helix for the activity of ZAR1 although some differences were noted that could reflect the different experimental set ups (CC domain vs full-length protein) as discussed in the paper.
Review contributors: Rachel J. Harding, Claudia Alvarez and Jacob McAuleyHuntington’s Disease Research Team, Structural Genomics Consortium, University of Toronto, CanadaNB: Review structure adapted from PreReview guidelines: https://prereview.org/users/164141/articles/200820-prereview-guidelines-how-to-write-a-preprint-reviewPreprint: https://www.biorxiv.org/content/10.1101/721191v1
The UIUC Plant Physiology journal club reviewed the preprint “α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2” (doi: https://doi.org/10.1101/708164) by Oltrogge et al. 2019. The paper describes the biochemical characterization of the CsoS2 protein involved in carboxysome assembly, identifying a repeat peptide region that makes weak electrostatic interactions with rubisco through the use of bio-layer interferometry (BLI) and x-ray crystallography. The authors identified evolutionary conserved residues through protein sequence comparisons and the sites of interaction between these residues and rubisco through protein X-ray crystallography. We found the paper to be very well written, well presented and valuable addition to knowledge about alpha carboxysome assembly. Our journal club assessed the paper as part of a learning exercise about how to make work accessible to a wide audience. Participants first learned about the “and-but-therefore (ABT)” model of paper writing popularized by Randy Olsen in his freely available book "Huston, we have a narrative", that can be used throughout the manuscript to help maintain the reader’s interest. Focusing on the abstract we found it to contain many of aspects of the ABT model. We also thought it could potentially be strengthened by including a stronger “but” phrase which generally represents the question under consideration. It was suggested that this phrase would start with the fact that there is little knowledge about how the carboxysome is assembled, and some members of the club questioned if the ongoing carboxysome engineering efforts might be mentioned as relevant to the wider importance of the work (either in the abstract or the discussion).One aspect we found particularly interesting was the similarities between CsoS2 and the algal protein EPYC which has been implicated in aggregation of rubisco in the pyrenoid. These appeared to us to an important point, and the reason to include information about CsoS2 as an intrinsically disordered protein (IDP) that could perhaps be emphasized more. As we were not familiar with the PONDR-FIT disorder score, we would have found it helpful to have a little more explanation as to its importance and interpretation. Overall we liked the approach for analyzing IDPs and thought it was an impressive effort to successfully crystallize the CsoS2 peptide with rubisco. In addition, we assessed the presentation of figures, we particularly liked the use of consistent colouring throughout, the choice of clearly legible font sizes on all graphs and the helpful diagrams to illustrate biochemical procedures, such as the BLI procedure in Fig 2b. One consideration is whether the choice of colors is colorblind friendly, using the app color oracle, several of the colors are indistinguishable in all the figures analysed. We also thought inclusion of legend titles would help guide readers on how best to interpret the data. We thought the X-ray crystallography data was presented in a clear and helpful manner, displaying what the individual residue interactions were between the bpeptide and rubisco. If it could be improved further it may be by inclusion of a label of rubisco for non-experts who may not immediately associate CbbL and CbbS as subunits. Finally, we particularly liked Figure 5 as it neatly summarized the proposed role of CsoS2 in carboxysome assembly.Other thoughts included:It would be interesting to include discussion of why the full length CsoS2 peptide does not appear to bind rubisco.The paper tied up loose ends and did a good job of using multiple approaches to build evidence for the direct interaction of CsoS2 and rubisco.
I argue that the academic publishing process as it currently exists is fundamentally antithetical to the advancement of science. Specifically, the way science is supposed to work is that the methods and conclusions of previous research can be scrutinized and improved upon. However, the static nature of articles published in academic journals under the current publication system creates the inaccurate impression that the article exists in its best possible state, without any changes that need to be made to it. It should be possible to publish a much smaller number of articles that can continually be updated and refined as new discoveries are made, instead of an unmanageably and bewilderingly large number of articles on the same topic. This would make it easier to point out and correct errors in a paper and to add results of new experiments as they become available. We no longer need to rely on a system centered around the enshrining of articles in academic journals in the same form forever. Now that such journals do not have to be published in print form, and collaborative scientific platforms like this one are becoming more popular, this is how all science should be conducted.