Boston University NeuroPreprint Journal Club
A spatial code in the dorsal lateral geniculate nucleusVincent Hok, Pierre-Yves Jacob, Pierrick Bordiga, Bruno Truchet, Bruno Poucet, Etienne Save doi: https://doi.org/10.1101/473520Version posted on Biorxiv: 11/19/18In the current work, Hok et al. report the existence of spatial receptive fields in the dLGN of rats that are similar in nature to HPC place fields. The authors demonstrate that dLGN place fields, which make up approximately 30% of extracellularly recorded dLGN neurons, are less stable and more variable (on a pass by pass basis) than their HPC counterparts. Further, the authors show theta oscillations in the dLGN local field potential and the presence of individual dLGN neurons that have theta rhythmic spiking. The authors report that, unlike CA3 neurons, most dLGN neurons do not exhibit theta phase precession suggesting that the dLGN spatial code does not carry sequential information about the animal’s current, past, or future trajectories. Finally, Hok and colleagues show that a sub-population of dLGN neurons can be modulated by visual stimulation but that this population does not overlap with neurons that exhibit place fields. Interestingly, dLGN place fields are insensitive to the presence or absence of visual information (as determined by similarity in responses in recordings from light vs. dark conditions) but remap when the color of the environment is altered (from all white to all black). By and large the results are robust and the reported findings will be of interest to researchers considering interactions between different forms of neural spatial representations and visual information. Further, the observation of spatial receptive fields in the dLGN raises important questions about fundamentals of visual processing. We enjoyed the manuscript and have the following suggestions for the authors.Major suggestions: • There is little discussion about dLGN visual sensitivity in the rat despite there being extensive literature on the subject. There is known retinotopy in dLGN (see for example, Montero et al. 1968). How, if at all, does this relate to the spatial response properties of dLGN neurons? For example, is there any correspondence between neurons that would be sensitive to the lower half of the visual field and remapping in the light vs. dark arena conditions? A similar question could be raised regarding the object sensitive sub-population. The authors should attempt to address the relationship between their observations and visual sensitivity of dLGN in more detail. • The object sensitive sub-population is intriguing, but the details concerning this finding are ambiguous. It is mentioned briefly in the main manuscript but the percentage of neurons exhibiting this tendency is unclear, even when examining the extended data concerning this observation. As a result, the reader is left a bit distracted by this information, especially when considering that object sensitive neurons are not place cells. The authors should consider presenting this component of the manuscript in greater detail. • The visual stimulation experiment is posed as a control for determining that dLGN place cells were indeed recorded in a visually sensitive area (dLGN), but this experiment was not conducted for CA3 neurons. How can we know for certain that the visual stimulation protocol wouldn’t have elicited modulation in CA3 neurons as well, thus rendering this component of the study inconclusive? • Tissue can often become displaced for extended periods of time when moving tetrodes along the D/V axis. How confident are the authors in the correspondence between their tetrode turning records and final tetrode placement? The waveform related analyses are pretty convincing and seems to cluster nicely into two groups, but waveform shape is not a definitive metric for determining the location of a recorded neuron. Is it possible to record from dLGN without moving electrodes through the hippocampus first? It would be helpful if the authors could provide more histology so readers can examine for themselves how displaced CA3 tissue was. • It seems that LFPs were primarily referenced to another tetrode. Instead, LFPs should be referenced against an electrode outside of either the hippocampus or dLGN such as a skull screw above the cerebellum. Because of the current referencing scheme and many other factors, theta oscillations recorded in the dLGN could be explained by volume conduction yet this is not considered. These issues may be of great importance to the theta phase precession analysis. Did the authors attempt to look at phase precession for dLGN place cells against both HPC LFPs as well as dLGN LFPs? If not, this would be an important analysis to consider. • No power spectral density plots are shown for theta oscillations in CA3 and dLGN. It would be interesting to see if the dLGN theta peak in the power spectrum is broader compared to CA3, which might explain the higher theta frequency and would also affect phase-related analyses. Additionally, a consideration of speed related modulation of theta dynamics should likely be included. Minor Concerns: • Table 1 should include a #/% of cells which were “object specific” • Re Overdispersion analysis (line 460): A linearly scaled Poisson distribution will itself be poisson distributed, not normal, with the approximation being more valid at higher firing rates. The Z value described here will therefore be biased to higher values for lower firing rate neurons. Because of this, it is unclear if the results in lines 90-92 are artificially strong or weak. If thalamic neurons have a higher firing rate than CA3 neurons, they may have an even higher difference in dispersion than reported. A consideration of percentiles rather than standard deviations would likely be revealing. • Quantification of the object rotation sub-experiment (lines 144-147) should be included in the main manuscript text. • More details on the properties of theta modulation in dLGN should be presented. What percentage of dLGN neurons had peaks in the theta frequency range in the FFT of their spike train autocorrelations (i.e. how many were significantly theta rhythmic)? What percentage of dLGN neurons were theta phase locked and was there a bias to a particular theta phase? Was theta oscillatory activity for single dLGN neurons modulated by running speed? • Was a velocity filter used when creating spatial firing rate maps? In a related point, did the authors examine potential differences in mobile vs. immobile activation for dLGN vs. HPC? • Perhaps we missed it, but what size was the smoothing kernel for 2D ratemaps (in cms)? • Did the authors examine the spatial distribution of dLGN place fields and, if so, were they uniformly distributed? It would be interesting to know if the fields clustered near objects for example. • The explanation of the “field index” metric is difficult to understand in the methods and should be clarified if possible. Figure 2: The color-coded pass index trajectory plots are not very informative because the dots are all layered on top of each other. Authors could do one or multiple of the following to enhance interpretation: make the dots smaller, make the dots transparent, make the color map sequential rather than qualitative. It would also be helpful to provide an “n” of the number of place cells in each region in Fig 2g. Figure 3: The close up of a single pass in the upper right corner of sub-plots 3b and 3c are confusing. The legend could be revised to clarify what we are looking at. In general, we are a bit unclear as to why the close up of a single pass is necessary. Are we supposed to see rhythmic activity in the spikes? The close up of a single pass is not useful for this because the rat may not be moving at a constant velocity. It may be the case that the spike train above is sufficient. - BU NeuroPreprint JC
PREreview-PLOS Open Access Week Preprint Journal Club Information
Join us for the OA Week PLOS/PREreview live-streamed preprint journal clubs! REGISTER HERESCHEDULEDONE! Neuroscience – Monday October 22, 2018 – 9am PDT / 12pm EDT / 4pm UTCPreprint: Sex Differences in Aggression: Differential Roles of 5-HT2, Neuropeptide F and Tachykinin Facilitators: Samantha Hindle (PREreview) and Daniela Saderi (PREreview)Expert: Dr. Tim MoscaCollaborative notes and info to join this call: Neuroscience EtherpadPREreview available here. DONE! Bioinformatics – Tuesday October 23, 2018 – 9am PDT / 12pm EDT / 4pm UTCPreprint: EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma Facilitators: Daniela Saderi (PREreview) and Monica Granados (PREreview)Experts: Dr. Shannon McWeeney and Dr. Ted LaderasCollaborative notes and info to join this call: Bioinformatics EtherpadPREreview available here. DONE! Ecology – Wednesday October 24, 2018 – 9am PDT / 12pm EDT / 4pm UTCPreprint: Host-parasite interaction explains variation in prevalence of avian haemosporidians at the community level Facilitators: Jessica Polka (ASAPbio) and Steven Burgess (University of Illinois)Expert: Dr. Timothée PoisotCollaborative notes and info to join this call: Ecology EtherpadPREreview available here.What are PREreview Live-Streamed Preprint Journal Clubs? #LivePREJC
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.
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
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!