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.
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. Here 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
PREreview of OA Week Live-streamed Neuroscience preprint JC
This is a review of the bioRxiv preprint "Sex Differences in Aggression: Differential Roles of 5-HT2, Neuropeptide F and Tachykinin" by Andrew N Bubak, Michael J Watt, Kenneth J Renner, Abigail A Luman, Jamie D Costabile, Erin J Sanders, Jaime L Grace, and John Swallow. DOI: https://doi.org/10.1101/407478 This review was compiled from discussion points raised during a PREreview live-streamed preprint journal club as part of Open Access Week, 2018. The 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: Dariusz K. Murakowski, Tim Koder, and Daniela Saderi.
Discussing the culture of preprints with auditory neuroscientists
I started writing this memo while on an airplane, flying back from sunny San Diego. While definitely one of the highlights of the trip, the sunshine was not the reason for my visit to Southern California. Instead, I was there with hundreds of other auditory neuroscientists from all over the world to attend the 41th MidWinter Meeting of the Association for Research in Otolaryngology (ARO).
Mozilla Mini Grant Application (June 3, 2017)
Here is how it all started. Two researchers and ASAPbio Ambassadors met at a Mozilla Working Open Workshop
in April 2017. A PhD student (Daniela) and a postdoctoral fellow (Sam) decided to volunteer some of their time to develop guidelines to help researchers from all around the world start preprint journal clubs. We believed this would have contributed positively to spreading the word and value of preprints in the scientific community, as well as helped early-career researchers master their skills in peer review.
During the Mozilla Science Global Sprint, June 2-3 2017, we wrote our application to the first Mozilla Science Mini-Grant. We asked for enough money to support 20 beta testers by covering the cost of snacks and beverage for two preprint journal clubs. And we were awarded
Since then, a lot has happened, including starting PREreview thank to the help of the Authorea team and the support of many others who share our mission.
Since July, our application has been posted on our project GitHub
, but we wanted to have it on PREreview as well. So below is our full proposal. Thank you!
UIUC Plant Physiology Journal Club: TPU and beyond. 2018/10/30
The UIUC Plant physiology journal club chose to review the preprint “Triose phosphate utilization and beyond: from photosynthesis to end-product synthesis” (http://dx.doi.org/10.1101/434928
), by McClain and Sharkey, about the role of phosphate levels in relation to CO2 assimilation during photosynthesis. The paper explains that when the rate of photophosphorylation which produces ATP, exceeds that of starch or sucrose synthesis which consumes ATP, phosphate levels drop causing photosynthetic electron transport rates to slow. This process is defined as Triose phosphate limitation (TPU).
We found the paper provided a very thorough definition of TPU and thought it was a really good introduction to the topic. In particular, the explanation about the way TPU limitation can be identified by no change in photosynthesis and decline in PhiPSII at high CO2 was very useful. The paper raises a number of points we were interested to discuss further including why TPU limitation is only slightly more than photosynthetic rate? Are some plants are more subjected to TPU limitation than others? Why is TPU limitation is slightly more than photosynthetic rate (one might predict that natural selection would select for utilization of all their photosynthate)? Why C4 plants do not experience any TPU limitation? Is it more common to see TPU limitation in Li6800s?
The question of the potential impact of a rising atmospheric CO2 concentrations on TPU is a fascinating topic. We thought it would be beneficial for readers to include reference to Experimental free air CO2 enrichment (FACE) experiments which have sought to address this issue, and some degree of guidance about what types of increases in atmospheric CO2 would be required to potentially see an effect.
In addition it would be useful to mention that many of the TPU studies have been performed in pot bound plants, which experience an altered shoot/root ratio creating an artificial sink limitation, and a bit more discussion about how often TPU limitation might occur under field conditions (Arp 1991). Finally it might be good to include a bit more discussion about how the xanthophyll cycle kicks in to protect the plant under stress and that decreased PhiPSII could be an example of non-photochemical quenching.
In summary, we thoroughly enjoyed the paper, we learnt a lot and look forward to seeing it published.
In equation 5 it is not entirely clear what the phi symbol is?
The symbol R is used to represent three different variables, could maybe consider changing this to prevent confusion.
Many color combinations used in the figures would be unsuitable for those with color blindness, and suggest using color oracle (https://colororacle.org/
) to help.
Fig 2: Clarification on what ‘a little’ and ‘a lot’ means would be helpful
Fig 2: We found it a bit confusing, many members were unclear about what it was demonstrating and suggest considering reformulating the description as we believe it could be useful as a teaching aid.
Fig 3: Many members really liked this figure and thought it provided a clear image to explain the various limitations a plant experiences during an A/Ci curve. There was some discussion about where the boundary lines were drawn, this might be addressed by having zones of colour fade into each other rather than represented as sharp boundaries. It was also suggested that some kind of upper bound to J limitation of ETR might be included (possibly fading out to white?)
OIST PREreview JC - "Disentangling unspecific and specific transgenerational immune priming components in host-parasite interactions"
Disentangling unspecific and specific transgenerational immune priming components in host-parasite interactions
Frida Ben-Ami, Christian Orlic, Roland R. Regoes
Overview and take-home messages:
In this study, the authors tackle the topic of transgenerational immune priming in invertebrates. The authors designed a large experiment taking advantage of clonal Daphnia to test whether infecting parental generations with different parasite strains improves the offspring's resistance to that parasite overall and if yes, if they resist that specific strain more effectively than other strains. This experiment essentially tests the specificity of immune priming at a very fine "strain" scale. The results did not support parental infection strain differentially affecting offspring resistance to different strains, suggesting that immune priming is not specific to the strain level in this system. However, a mathematical model the authors developed for that study fits the data exceptionally well, which means this model could potentially be used in a predictive manner for this or similar systems. Additionally, the unexpected result that one strain actually facilitates specific infection in the offspring is surprising and opens the door to additional inquiry and future experimentation. Overall this study is very interesting and well-presented, but there are a few concerns that could be addressed and improved in the next version of the manuscript.
Live streamed Journal Club on "Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level"
This is a review of the bioRxiv preprint "Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level" by Luz Garcia-Longoria, Alfonso Marzal, Florentino de Lope, and Laszlo Garamszegi. DOI: https://doi.org/10.1101/432260 This review was compiled from discussion points raised during a PREreview live-streamed Ecology preprint journal club as part of Open Access Week, October 24, 2018. The 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: Dariusz Murakowski, Irene Ramos, Dena Emmerson, Adéla Nacer, Asar Khan, and Daniela Saderi.