Preprint Journal Clubs: Your Opinions Revealed
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.
PREreview: Meet Our Advisory Committee
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.
Present and past LivePREJCs: PREreview's community live-streamed preprint journal clubs
Hello PREreviewers! Below is a list of upcoming live-streamed preprint journal clubs (LivePREJCs) as well as those hosted in the past. To learn more about what to expect and how to solicit our help to organize one, please read here.
UIUC Plant Physiology JC (2018/12/3): Revisiting tradeoffs in Rubisco kinetic parameters
The preprint “Revisiting tradeoffs in Rubisco kinetic parameters” by Flamholz et al. 2018 (https://doi.org/10.1101/470021) investigates the tradeoffs between catalytic efficiency and rate, of the central enzyme in carbon fixation, Ribulose-1,6-bisphosphate Carboxylase/Oxygenase (RuBisCO), using kinetic modelling based on biochemical data. The manuscript builds on previous work from the group (Savir et al. 2010; doi: 10.1073/pnas.0911663107), including an expanded dataset of kinetic parameters of ~250 RuBisCOs from 286 different species extracted from the literature. We thought it was an important topic with potential interest for a wide range of researchers working on photosynthesis and evolution.The main questions the paper seeks to address are:Which trade-offs are inherent in Rubisco kinetics. Has evolution resulted in optimal kinetics within the constraints of those inherent trade-offs.The preprint challenges the theory that increasing RuBisCO activity reduces enzyme specificity as described by Tcherkez et al. (2006), which was based on a model of enzyme activity the discriminates between CO2 and O2 in a transition state. Data supporting this theory has been reported widely in the literature. However, the authors propose that there is little/no correlation between specificity and activity, and most previously-found correlations (KcatC and SC/O etc) are smaller for the new dataset, except for KcatC/KC and KcatO/KO. We really enjoyed reading the manuscript and as it challenged our preconceptions about RuBisCO activity. We found it interesting (and surprising!) that the data contradicts a well established theory, and it increased our awareness out current models of enzyme activity. We also thought it was interesting that they were able to collect data from so many species across many previous studies and also break down trends/relationships between different clades or physiologies. It was also interesting that given that they were using data from studies that showed the opposite, they were able to come to the conclusion they found. We particularly liked the authors suggestions about how to move the field forward and the call for an improved understanding of RuBisCO kinetic mechanism.There were a few areas we thought it would be useful to clarify:Providing a cartoon model of the proposed mechanism would help readers unfamiliar with the nuances of the models being assessed. More information about how the authors selected and filtered data collecting from the literature and how the different datasets were taken into account in statistical analysis. i.e. how many measurements per species, types of values (mean/median) etc.Figure 4 and 5: how was the conclusion reached that there was no correlation between parameters?Organization, it would make things stronger to layout the arguments clearly between what came before and after, for those not familiar with the academic argument.As the paper argues against what most people are reading it might expect, additional text theorizing why this is the case would be useful to guide readers.Minor commentsFigure 2A y-axis labelsPut a key at the top as the symbols can get buried in the text
OIST E&E PREreview JC "Biodiversity trends are stronger in marine than terrestrial assemblages"
Biodiversity trends are stronger in marine than terrestrial assemblagesShane Blowes, Sarah Supp, Laura Antao, Amanda Bates, Helge Bruelheide, Jonathan Chase, Faye Moyes, Anne Magurran, Brian McGill, Isla Myers-Smith, Marten Winter, Anne Bjorkman, Diana Bowler, Jarrett EK Byrnes, Andrew Gonzalez, Jes Hines, Forest Isbell, Holly Jones, Laetitia Navarro, Patrick Thompson, Mark Vellend, Conor Waldock, Maria DornelasbioRxiv, October 30th, 2018doi: https://doi.org/10.1101/457424Overview and take-home messages:Blowes et al. tackle an impressive and large undertaking in this paper by attempting to disentangle global biodiversity trends through a meta-analysis of data from 358 studies. By dividing the available data by biome and taxa, the authors were able to detect different biodiversity trends in marine and terrestrial biomes. Tropical marine biomes, particularly the Caribbean, have a more negative deviation from the mean trend in species richness and more positive deviations from the overall trend in species turnover--species are turning over more quickly in marine biomes. The analyses demonstrate that mean local species richness is not decreasing, but many individual regions deviate significantly from the overall mean. The results have important implications for how we discuss changes in biodiversity in the anthropocene, but it is important to make clear that locally static species richness does not equate to globally static species richness, and species are going extinct at an alarming rate. Overall, this paper presents careful analyses and is clearly written, however, there are a few issues that, if addressed, we feel could improve future versions of the manuscript.
Live-streamed preprint Journal Club on "EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma" – October 23, 2018
This is a review of the bioRxiv preprint "EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma" by Borong Shao, Maria Bjaanæs, Åslaug Helland, Christof Schütte, Tim Conrad, doi:10.1101/410472. This review was compiled from a discussion during the live-streamed Bioinformatics preprint journal club as part of an Open Access Week effort organized by the PREreview team and PLOS. Event details can be found here, and the collaborative Etherpad showing all the journal club notes can be found here.In addition to those named as authors above, the participants who wished to be acknowledged for their contributions to this review are as follows: Samantha Hindle, Paul Goetsch, and Bradly Alicea.
PREreview-PLOS Open Access Week Preprint Journal Club Information
Join us for the OA Week PLOS/PREreview live-streamed preprint journal clubs!
DONE! Neuroscience – Monday October 22, 2018 – 9am PDT / 12pm EDT / 4pm UTC
DONE! Bioinformatics – Tuesday October 23, 2018 – 9am PDT / 12pm EDT / 4pm UTC
DONE! Ecology – Wednesday October 24, 2018 – 9am PDT / 12pm EDT / 4pm UTC
What are PREreview Live-Streamed Preprint Journal Clubs? #LivePREJC
MozFest 2017 Session– Changing the scientific publishing ecosystem: preprints and beyond
The following notes were taken by Naomi Penfold, eLIFE Innovation Officer, during our session at MozFest 2017
is a link to our short slide deck.
Welcome everyone! We are excited to see you and we hope you are having a fantastic time at MozFest 2017.
Who are we?
* Daniela Saderi, neuroscientist at OHSU. I love organising community events, including Science Hack Day Portland. Originally from Sardinia (it's beautiful!)
* Samantha Hindle, "post"-postdoc at UCSF, from scarborough, UK. I'm a neuroscientist too.
We are ASAPbio ambassadors! We advocate for preprints in the life sciences, and have built PREreview to enable researchers to review preprints in their journal clubs and online.
* Naomi Penfold, eLife - I'm here to help Dani and Sam to encourage the adoption of preprints.
Neurobiology and Reproducibility Journal Club
Gender and international diversity improves equity in peer review Dakota Murray, Kyle Siler, Vincent Lariviére, Wei Mun Chan, Andrew M. Collings, Jennifer Raymond, Cassidy R Sugimoto bioRxiv, v1 (August 29 2018) https://doi.org/10.1101/400515