Great read. The process (and the friction it brings) matters, and cutting too many corners turns users into glorified middlemen rather than experts. Scientific pursuits are never guaranteed to be fruitful (at least when done rigorously), so the optimal choice imo is to emphasize learning and growth.
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
So...my undergrad thesis student is doing a quality analysis of studies found in meta-analyses. She identified a few and we contacted the authors to request their effect sizes and other variables for the studies in their papers.
Here's what happened:
scientiapsychiatrica.com/index.php/Sc...
Having explored (to a small extent) what we can do with Xenium data, we hope to dig deeper into biological insights. We look forward to combining this with the growing suite of available, collaborative tools for analyzing ST data.
Our code is available here: github.com/jmkotah/xeni....
We did this using a relatively crude threshold segmentation of IBA1 fluorescent signals to selectively allocate neuroimmune transcripts. Importantly, we expect this to be compatible with more advanced segmentation methods, which can be used to maximize the data obtained from imaging ST data.
Because the Xenium platform nicely allows for post-run immunostainings, we showed proofs-of-concept that registering and segmenting post-run images can be used to direct transcript allocation to cell types of interest, and that 'leftover' transcripts outside masks can be re-allocated.
We used the tools provided by geopandas to try different ways of allocating transcripts, and found that simply expanding the nuclear borders (as determined by DAPI) can have consequences, e.g., for cell type annotations. On the other hand, the strict nuclear border leaves a lot of data on the table.
I'm very happy to share that our work describing a geospatial approach to allocating transcripts for single cell spatial transcriptomics (in human brains) using the 10x Xenium platform is now out in @commsbio.nature.com! @barteggen.bsky.social @kooistrasm.bsky.social
www.nature.com/articles/s42...
There's a movement in neuroscience suggesting we should be pursuing bigger bets with larger teams. I think there's a case for doing a bit of this, but I think it's a bad idea to prioritise it for two reasons, and a good case for saying we should be moving in the exact opposite direction. 🧠🧪
Are you using 5xFAD mice to study Alzheimer’s disease? Our work out today @cp-neuron.bsky.social may be relevant to you 🐁🧠 Age and sex are known to influence Aβ plaque burden in these mice. Here, we found that the transgene parentage is another strong determinant.
Thread below: (1/11)
🚨New paper out in Nature Mental Health from my work with @erindunnscd.bsky.social at #MassGeneral! We found that childhood adversity leads to #epigenetic changes that can increase OR reduce risk for depression. Let me explain... 🧵(1/6)
Read the paper here: www.nature.com/articles/s44...
Happy to share that our work on the impact of stress on human milk microbiome is now published in BBI! Great work lead by Hannah Juncker!! www.sciencedirect.com/science/arti...
Wishing the Elsevier editors who desk-accepted this all the best for their next career moves.
doi.org/10.1016/j.ij...
go.bsky.app/Lyzro3M
!WELCOME!
thought we might need a starter pack for all those coming over from the birdhouse - here's a GliaSky list.
apologies for missing many of you - please do reply to get added
and remember to repost so the newbies can find us!
