@moritz_negwer@mstdn.science avatar

moritz_negwer

@moritz_negwer@mstdn.science

Neuroscientist by training, tinkerer by nature. Now scanning transparent mouse brains with light-sheet microscopes. Microscopy, clearing, data crunching, tinkering.

Working as postdoc at https://mastodon.nl/@radboudumc with Nael Nadif Kasri and Corette Wierenga, looking at neuron-distribution differences in mouse models of ASD.

Married, father of one. Toots in English, German, Dutch.

opted into tootfinder for full-text indexing. Check it out: https://www.tootfinder.ch/index.php?join=1

This profile is from a federated server and may be incomplete. Browse more on the original instance.

jonny, to random
@jonny@neuromatch.social avatar

What other disciplines have an extremely strong set of visual icons and imagery like neuroscience? I assume "all," but eg. In neuro we have

the sagittal human brain shape,
the 2d blobby neuron (usually pyramidal-ish with projections ~1-2x body diameter),
graphs/networks (ok this is lots of things but ours usually have visible/larger than average nodes)
For icons, for visual style we have the cajal sepia/black monochrome... etc.

Definitely my bias but its easier for me to imagine a neuron icon than like an earthquake or metaphysics icon. I also wonder whose iconography would be the most illegible to ppl outside it (and why is it going to be number theory)?

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny Earth sciences has the pale blue dot, and the hockey stick temperature graph.

(I guess a good first approximation could be "how many emoji can a scientific field claim for itself?")

moritz_negwer, to Neuroscience
@moritz_negwer@mstdn.science avatar

Clever neuronal activity labelling strategy: Engineered Ca2+ sensor biotinylates nearby proteins. Those proteins can then be stained - works for single vesicles, organelles, dendritic compartments, all the way to neuronal engrams. Both in culture and in vivo!

Molecular recording of calcium signals via calcium-dependent proximity labeling
Kim et al., Nature Chemical Biology 2024
https://doi.org/10.1038/s41589-024-01603-7

(preprint version: https://www.biorxiv.org/content/10.1101/2022.07.14.500122v2.full)

#neuroscience #MemoryEngram #neurobiology

moritz_negwer, to Neuroscience
@moritz_negwer@mstdn.science avatar

LAMP1 protein-tracking with clever use of proximity labeling reveals neuron-specific Lysosomal function.

Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons
Li et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.16.594502v1?ct=

azonenberg, to random
@azonenberg@ioc.exchange avatar

TIL that if you have a large enough input dataset, it's possible for the NIST MIST plugin for ImageJ to generate a TIFF file >2^32 bytes in size.

Except this isn't allowed by the spec since all of the pointers to offsets in the file are 32 bit.

If you then attempt to open this malformed file in GIMP, it will appear to load normally until it hits some point a bit past the 4GB boundary, at which point you get some kind of integer overflow or something.

I'm not sure what happens next because my machine with 128GB RAM froze up for a while and ultimately GIMP got oomkilled. But nothing good, that's for sure.

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@azonenberg Hm, seems like you have hit the edge of what TIFF can do. Would it be worth your time to switch to a different format (and viewer as GIMP can't handle those)?

E.g. ome-tiff (https://www.openmicroscopy.org/ome-files/) or zarr (https://ome-zarr.readthedocs.io/en/stable/) or so, those can be tiled/chunked and therefore should be easier on your RAM. GIMP can't read those but Napari (or ImageJ itself, with with appropriate plugins) should be able to.

erinnacland, to science
@erinnacland@fediscience.org avatar

"Fewer U.S. scientists are pursuing postdoc positions, new data show" 📉

"The trend underscores concerns that the academic community is facing a postdoc shortage and that early-career scientists are increasingly favoring higher paid positions outside academia."

“It’s not a situation that’s good for the country.”

@academicchatter via @klangin https://www.science.org/content/article/fewer-u-s-scientists-are-pursuing-postdoc-positions-new-data-show

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@erinnacland @academicchatter @klangin #IchbinHanna folks, take note. I wonder whether something similar is happening in Europe.

moritz_negwer, to Neuroscience
@moritz_negwer@mstdn.science avatar

about , the roadies of the brain!

PhD student Imke Schuurmans and team have come up with a comprehensive one-step protocol for turning human directly into functional Astrocytes, and how to co-culture them with induced human neurons on multi-electrode arrays for .

From my new group (Nadif Kasri lab @radboudumc @DondersInst)

Preprint: https://www.biorxiv.org/content/10.1101/2024.03.27.586938v1

Imke's explainer: https://www.linkedin.com/posts/imke-schuurmans-b713a6105_astrocytes-mea-activity-7180850761176645634-qNVm

jonny, to random
@jonny@neuromatch.social avatar

Biologists please take a month and learn to use multilevel models. In most conditions you cant treat individual cells or synapses as independent measurements for a statistical test, but you also dont have to throw that data away by using a per-organism mean only. Im sure theres some new hotness in modeling software since I had to use it, but lme4 uses almost the same syntax as R's lm
https://pubpeer.com/publications/98FCB4581543F4A4D1BE2F386D6BDA

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny I'm probably in the target group for this haha. Biology as a field is notoriously lax with statistics and I'm suspecting we took the wrong lessons from reproducibility crises in e.g. psychology.

I myself have only recently started doing my (still comparatively simple) stats in python so I can do multiple-comparisons correction at least. I figure I could get more out of my data with multilevel models too. Any recommendations for a good python package in that direction?

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny No worries, I didn't take it as personal. And you are right, most of biology treats statistics as a bit of an afterthought. I have seen well-publishing research groups that mostly use Excel's =TTEST() for everything. Probably the biggest real-world improvement (well, besides better training) would come from Excel introducing a multi-level statistics function 😅

Re: python packages, this one seems to look about right. More pointers are welcome of course :) https://www.statsmodels.org/stable/generated/statsmodels.regression.mixed_linear_model.MixedLM.html#statsmodels.regression.mixed_linear_model.MixedLM

azonenberg, to random
@azonenberg@ioc.exchange avatar

My German is somewhat limited but I'm pretty sure this is a tech school.

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@azonenberg It does say "Hochschulsport" which would imply a university. Probably the local Ruhr-Universität Bochum?

impactology, to random
@impactology@mastodon.social avatar

Is there a course on how to create a small server farm, data center powered by solar?

Not talking about self-hosting here, but rather on how to create and assemble a team for building a small business of selling compute, storage

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@impactology I imagine the folks will have to say something about this

inquiline, to history
@inquiline@union.place avatar

Anyone happen to know specifics about the manufacture and/or discard of toner cartridges? Say 1980s-present? What firms manufactured them, where, what's the ink made of, etc? (student is wondering and I'm being )

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@inquiline Interesting question, hard to google. I figure Xerox made their own back in the day.

Some wikipedia browsing suggests that Canon manufactures print engines (and toners) for themselves and for HP: https://en.m.wikipedia.org/wiki/HP_LaserJet

Kyocera for themselves too: https://en.m.wikipedia.org/wiki/Kyocera

BorisBarbour, to random
@BorisBarbour@mastodon.social avatar

This investigation of Ranga Dias' superconductivity publications is remarkable for multiple reasons.

https://www.nature.com/articles/d41586-024-00716-2

Nobody comes out of it well, but Nature are much more transparent about the editorial process than I can ever remember. (It's a little unclear if that was spontaneous, but, if not, the frequently claimed independence of Nature News came good.)

Thread. /1

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@BorisBarbour Good write-up, thanks. That's what I find most striking as well, Rochester University only got around to ask the grad students on the fourth investigation. What were they checking in the previous rounds, I wonder?

elduvelle, to privacy
@elduvelle@neuromatch.social avatar

Antivirus has been collecting and selling their users’ browsing information 😱😱😱

I need to change my antivirus ASAP!! What do you all recommend?!

From: @jon
https://social.vivaldi.net/@jon/111985903331842810

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@david_megginson @elduvelle seconding this, Windows' built-in anti-malware tool is already there and seems to work decently. It's what I use on the Windows portion of my Win/Linux dualboot.

If you don't already, another useful idea would be to install adblockers (i.e. uBlock origin) on all browsers you have. Makes for a much quieter browsing experience and reduces your attack surface a bit, as advertisements can be used as malware vectors (see here: https://en.m.wikipedia.org/wiki/Malvertising ).

impactology, to random
@impactology@mastodon.social avatar

As the 'Delhi Chalo' protest by farmers entered its second day, Indian Farmers Fly Kites To Tackle Drones Carrying Tear Gas Shells

Using the long strings of kites to entangle the rotors of the drones, potentially causing them to crash.

https://www.youtube.com/watch?v=xXmJonn2IOs

The farmers, primarily from Punjab, have been steadfast in their determination to march towards Delhi, demanding a legal guarantee for the minimum support price (MSP) and other agricultural reforms

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@impactology

"Protesting Farmers crash Police Drones with Kite Strings" is such a cyberpunk headline. We are truly living in the future now.

Also interesting how farmers all across the world seem to be protesting right now, see also: All of Europe. Every country has national grievances of course, but I wonder whether it's compounded globally by historically high natural gas prices (= fertilizer prices go up) and rainfall disruptions from El Niño and the climate crisis.

moritz_negwer, to Neuroscience
@moritz_negwer@mstdn.science avatar

Cool new paper: PNNs regulate excitatory input on PV+ cells (in NAc at least):

The Perineuronal Net Protein Brevican Acts in Nucleus Accumbens Parvalbumin-expressing Interneurons of Adult Mice to Regulate Excitatory Synaptic Inputs and Motivated Behaviors
Hazlett et al., Biological Psychiatry 2024
https://doi.org/10.1016/j.biopsych.2024.02.003

futurebird, to random
@futurebird@sauropods.win avatar

Are there therapists who specialize in helping children who are stressed out giving tech support to their parents?

My mom is a mathematician. She can program w/ punch cards. But, she & Dad just don't keep up with tech anymore. Drives me nuts.

Gave my dad an iPhone for Christmas. They HATE it. Probably would hate any phone. Now they say it's recording their conversations.🙄

Dad holds down the buttons on the side when he picks it up. Activates the voice assistant... they think it's a hacker.

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@futurebird @kritischelezer This is going to fast become very common, I think. "Parental controls" carries a lot of implicit baggage, maybe a better term would be something like "caregiver options" or so?

Semantics aside, I think one of the frustrating things about old age is the gradual loss of dignity. Now many basic functions of life are mediated by tech, those too carry some dignity. And those too can be lost. We haven't really grappled, as a society, with the consequences.

chargrille, to random
@chargrille@progressives.social avatar

"Rowledge, a hunter & businessman, has been talking about & tracking the spread of the brain-eating disease for nearly 30 years & advocating for government action with limited success."

“The border won’t stop this disease...

This is a highly fatal & contagious disease that humans created. Absent a miracle, it’s an extinction event for deer...devastating threats for trade & our economy, & the possible implications for human health are all but unthinkable.”

https://thetyee.ca/Analysis/2024/02/06/Zombie-Deer-Disease-Bad-As-Sounds/

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@chargrille Oh wow, that's hella scary. Deer now are reservoir species for:

Deer-to-human CWD transmission has not been shown yet, but as his article notes, there is no principal reason why it shouldn't be possible. https://www.sciencedirect.com/science/article/pii/S1567134820303154

eharlitzkern, to academia
@eharlitzkern@historians.social avatar

Submitted a work order to Facilities because there is a loud white noise in one of my classrooms. I am now being CC'd on every email as my work order is being passed around among people and departments and no one wants to do the job. And for every email, more and more people are being CC'd. 😁

I mean, who needs entertainment? Also, this explains SO MUCH about what is going on (or not going on) at this university.

@academicchatter

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@eharlitzkern @academicchatter That sucks, I hope one lone idealist sticks their neck out and gets something done.

I've observed that besides anything else they do, modern administrations are fantastically skilled at diffusion of responsibility. Your problem is bounced around until the entire institution has given it a good hard look and declared it "not our reaponsibility". Note that fixing your actual problem is strictly optional in this framework.

MartinEscardo, to random
@MartinEscardo@mathstodon.xyz avatar

So I measured and computed the cost of electricity to run my ebike to commute to work.

I do 8 miles per day, for about 20 days a month.

The ebike charges at 90kwh for less then 3 hours each day.

The cost is less than £2 per month, or $2.50 USD. I am surprised.

moritz_negwer,
@moritz_negwer@mstdn.science avatar

I think we have an SI prefix error in the capacity.

My ebike's battery is a medium-sized Bosch system with 400Wh (i.e. 0.4kWh) capacity, good for ca 80 km in normal use.
90 kWh is closer to a Tesla (or two base model Kia e-Niro).

@MartinEscardo could it be that the charging is at 90 Wh (without the k)? Then the maths would make more sense, you'd have ca (90 Wh * 3h * 20 days) = 5400 Wh per month, or 5.4kWh. That would be pretty close to @johncarlosbaez 's calculations of 6 kWh.

ninokadic, to Cognition
@ninokadic@mastodon.social avatar

What's your position regarding consciousness? Broad physicalism (we'll have a scientific explanation one day) or broad anti-physicalism (science can't give a complete account)? Or something else?

Please repost after voting, I'm genuinely curious! 🤔

@philosophy @philosophyofmind

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@ninokadic @philosophy @philosophyofmind

Interesting discussions here. My (cellular neurobiologist's) intuition would roughly be: I'm optimistic about our ability to find a reasonable set of measurable markers for consciousness in humans.
I'm considerably less optimistic about us agreeing on an explanatory framework, let alone its validity beyond humans. It's too easy to get lost in semantics, IMO.

(Mostly writing this to smuggle this webcomic into the conversation: https://dresdencodak.com/2009/01/27/advanced-dungeons-and-discourse/ )

jonny, to random
@jonny@neuromatch.social avatar

I love the academic perception of time. We dont have enough time to spend a month writing tests and docs to make a project maintainable, but its no problem to throw 5 years of labor into the trash when someone leaves the lab and nobody understands what they did

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny Very true. Somehow everyone seems to be not just time poor, but time destitute.

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny (Tangentially related to this, I recently re-read one of my favourite children's novels (Momo by Michael Ende, of Neverending Story fame), and the story is quietly subversive.

The bad guys are anonymous grey gentlemen in business attire who convince everyone to "save time", which they then hoard for themselves and smoke as cigars.

Those grey gentlemen are the scarcity mindset personified, and gain control by making everyone voluntarily making themselves time-poor.)

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny Well said. As a positive example I'd posit the Allen Brain Institute - they seem to be industrializing another branch of neurobiology every year or so, with open data and pipelines and decent documentation, to the benefit of the entire field.

(It's probably telling that it got started by a gigantic private donation, not project-wise funding.)

I'm not sure we have a good way to properly value infrastructure building anywhere. Are there domains outside of science that do this better?

moritz_negwer,
@moritz_negwer@mstdn.science avatar

@jonny That's an interesting perspective, I have only ever seen their work from the outside.

Maybe the Allen is to neurobiology what CERN is to particle physics? A data-intensive big-rig center, generating a surplus of data for theorists around the world to interpret. The physical infrastructure is concentrated in one place, but the data is disseminated and will hopefully inform experiments everywhere. Now we only need to have ubiquitous data-science training for biologists so they can use it.

moritz_negwer, to TwitterMigration
@moritz_negwer@mstdn.science avatar

Good news (for once!) from dutch politics:

The Dutch Minister for digitalization has stopped posting on X because the platform refuses to follow Europe's rules.

Instead, she still posts on the fediverse on the government's own instance @avhuffelen and also on linkedin.

https://social.overheid.nl/@avhuffelen/111838461667688167

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