Bugra Özdemir

[Constantin Pape @cppape]

Check out the latest @neuro_beyond with me as a guest! We talk about a wide range of topics, from image analysis for microscopy to latest developments in AI.

[Deniz Saltukoglu @DenizSaltukoglu]

Thank you @BPoD_s for choosing our 4D B cell imaging and analysis as part of Beautiful Biomedical Pictures of the Day!

[Frank Han MD 🇺🇦Pediatric/ACHD/GUCH Cardiologist @han_francis]

Here's the scoop on all the heart statistics you ever wanted to know about the COVID vaccine @LovemycountrySd . #CovidIsntOver

This addresses the allegation that heart diseases of various types have been increasing after the rollout of the COVID vaccines from multiple perspectives.

Note that pericarditis, myocarditis, heart attacks, heart failure, and myocardial infarction sound the same to the uninitiated, but they are five different things. For example, if someone claims to you that a child is having a heart attack, in most cases they are wrong.

1. First, the overall deaths: "There as been no statistically significant change in card arrest deaths under 35, ever."
https://t.co/46eRzobMmd

2. Next, COVID vaccines continue to protect effectively against severe disease, especially when the base rate fallacy is taken into account. https://t.co/UwtTTJoIAF

3. Next, the risk of myocarditis is substantially higher after SARS-CoV-2 infection in unvaccinated individuals than the increase in risk observed after a first dose of ChAdOx1nCoV-19 vaccine, and a first, second, or booster dose of BNT162b2 vaccine (measured in England). https://t.co/srCHTysF7B

4. Next, you are gaining quite good protection from COVID related excess death when vaccinated:
https://t.co/kkKMo7AvGw

5. Next, there is no significant correlation in cardiac arrest deaths with the COVID vaccine, but there is a correlation with COVID disease: https://t.co/3mkZNum22M

6. Next, the amount of myocarditis deaths in young adults in the US has decreased:
https://t.co/NH0FtfOebM

7. Next, the amount of deadly myocarditis dropped with vaccine rollout in the US (when it previously increased in 2020): https://t.co/kb9yMM57Ae

8. To keep me honest, I do also include upsetting results such as the really well done study from South Korea detailing COVID vaccine myocarditis related severe cases and deaths; while the study does not directly explain why the reported the highest rate of severe myocarditis the rate is so high, the reason from prior experience of the cardiology ecosystem is typically genetics: https://t.co/qy3ATL6UNr

9. Increased risks and excess burdens of new-incident cardiovascular/cerebrovascular complications were reported among infected individuals; risks can be attenuated with vaccination and boosting . https://t.co/sq85GP9s2z

10. The relative risk of vaccine myocarditis varies by age and is most prevalent in the teen boys and yong men (citations CDC ACIP).

11. Yes the 2023 meta-analysis by Alamis group did claim to find more myocarditis in the vaccinated, but in order to do this all the vaccine myocarditis was counted, and all the COVID cases were excluded https://t.co/J1tcWHe0pv

12. Good news for kids - while cardiac complications are indeed rare for kids after COVID infection, their risk can be decreased further by geting vaccinated for the first time (also reference Patone) https://t.co/JMsl8r4s4b

13. Vaccination for COVID associated with lower post COVID cardiac complications: https://t.co/wGkOzCdN6x

14. COVID-19 vaccination was associated with significant reduction in all-cause hospitalization rates and mortality rates : https://t.co/EJLtcSVZ3y

[Constantin Pape @cppape]

Our micro_sam preprint is out! We finetune Segment Anything for Microscopy and build interactive napari annotation tools based on it. See preprint at https://t.co/pY7QvJPxDR, software at https://t.co/qbds1orDnK and more info in this thread.

[Josh Moore @notjustmoore]

Out now! "#OMEZarr: a #CloudOptimized #BioImaging #FileFormat with Int'l #Community Support" 😍

Huge thanks to the 68 co-authors, across 32 institutions (see the quoted tweet) 🙌

If you use #OMEZarr & weren't involved, let's start the next report! 📝

https://t.co/iSFOr3RYYU

[Marcelo Leomil Zoccoler @zoccolermarcelo]

Kota Miura @cmci_ giving the kickoff talk introduction to #BioimageAnalysis for the Defragmentation TS2 @NEUBIAS_ at Porto! Nice sushi analogy ⚔️🍣➡️💻📈

[Robert Haase @haesleinhuepf]

Highly recommended! 🔬🖥️👨‍🔬👇

[Deniz Saltukoglu @DenizSaltukoglu]

Nice way to start 2023 :) Pleased to announce that our lattice light sheet study on B cell surface features and IgM B cell receptor localization is out in EMBO Journal. Many thanks to our collaborators, @Bugrazdemir12, Michael Holtmannspötter, @KurreRainer, @ReskiLab, @PiehlerLab

[Riley Goodside @goodside]

OpenAI's new ChatGPT explains the worst-case time complexity of the bubble sort algorithm, with Python code examples, in the style of a fast-talkin' wise guy from a 1940's gangster movie:

[Bugra Özdemir @Bugrazdemir12]

Happy to see our review on cytoskeleton segmentation methods online! https://t.co/egA16fzLxz

[William Gibson @wgibson]

I can't believe I'm saying this this year, but I think this might be bigger than RNA vaccines.

DeepMind can effectively predict protein structure with the fidelity of crystallography.

https://t.co/HWeutGAsMK

[Ricardo Henriques @HenriquesLab]

Paper out =). #vLUME harnesses the best neural-net - the Human Mind - giving it an immersive VR environment to interpret 4D single-molecule data. An honour to work with @VRI_Daniel @AnoushkaHanda @christlet @SteveTheChemist @lumeVR and others. Check it: https://t.co/GHYLzr1VOW

[Ralf Reski 🇩🇪🇪🇺 @ReskiLab]

A NanoFE Simulation-based Surrogate Machine Learning Model to Predict Mechanical Functionality of Protein Networks from Live Confocal Imaging.
@pouyasgharzadeh @Bugrazdemir12
https://t.co/DqlnZiPPju

[Stefan A. Rensing @RensingStefan]

The protein from outer space: https://t.co/HRpFPiNIS0 'composed of anti-parallel beta strands of glycine, each of 15 to 17 -residue length, with about
20% oxidation to hydroxy-glycine, and termination at each end with an iron atom directly
bonded to C and N terminals'

[Kareem Carr, Ph.D. @kareem_carr]

people think training multiple models on data is some kind of crazy math thing. yet it’s basically this https://t.co/Bz3R9NefuM

[Nathan Shaner 🏳️‍🌈 @NathanShaner]

As it turns out, Aequorea fluorescent proteins aren’t limited to GFP... our lab’s first preprint, so we had to make it a good one, hope you enjoy 🙂🌈
https://t.co/AmE5H3Q8f0

[Andrew York @AndrewGYork]

Microscopy technique development's exploding, but core facilities still buy confocals. This ugly baby will end that.

Less phototoxicity, WAY faster than confocal. NO DRAWBACK.

Details here: https://t.co/xnyeN0OF0T

Co-invented by @amsikking.

Get one from [email protected]

[Rory Cooper @rorylcooper]

Here you can see ~80 day old shark embryos developing in a 6-well plate. Removing embryos from their egg cases allows us to observe and even manipulate their development 🦈🔬

[Sophien Kamoun @KamounLab]

A pentangular plant inflammasome by @jonathandgjones & Jeff Dangl https://t.co/aMYP3mSEts