Jake Vogel
@_JakeVogel_
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Neuroimaging guy, Philadelphia sports fan, beer, open science.
Philadelphia, PA
Joined February 2019
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‼️ Paper alert ‼️
"Deciphering the functional specialization of whole-brain spatiomolecular gradients in the adult brain" now published in PNAS!!
How is brain function organized? Regions vs. gradients? Geodesic vs geometric? We add to the debate!
1/
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Big news!! I've decided to turn down (!) an NIH K99/R00 and instead take a tenure track position at
@lunduniversity
!! I will be opening my own lab by the end of this year, which will use machine learning and multi-omic and imaging data to study ADRD. 🎉🎉🎉
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Does Alzheimer’s disease pathology spread through the brain consistently across the population? We delve into this in our paper “Four distinct trajectories of tau deposition identified in Alzheimer’s disease”, now online at Nature Medicine. Thread below 1/
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New preprint: Is there a typical progression of Alzheimer’s pathology? We characterize the spatiotemporal spread of tau from over 1500 tau-PET images and do not find one predominant pattern, but rather four separate patterns. 1/3
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What an honor it was to receive this award, and to meet her Majesty, Queen Silvia of Sweden! If you haven't noticed, there is some really exciting Alzheimer's work being done here in Sweden. It feels amazing to be a part of it!!
The young researcher Jacob Vogel at Lund University receives the H.M. Queen Silvia's Prize for a young Alzheimer's researcher in a ceremony at the German Church, Stockholm.
@Alzheimerfonden
#Alzheimer
#alzheimersdisease
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Mouse models of AD probably ain't it. 🐭 BUT! This week saw three interesting stories of AD or tau pathology occurring naturally and spontaneously in the animal kingdom. Should be worth our attention!
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‼️ Preprint alert ‼️ "Conserved whole-brain spatiomolecular gradients shape adult brain functional organization"
Morphogen gradients interact to produce functional 🧠 areas during early development. Can we detect them in adult brains?
A 🧵 1/17
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Very excited to present our new work in Nature Communications. We identified a pattern of genes expressed systematically along the A/P axis of the human hippocampus. The pattern also informed hippocampo-cortical interactions. 1/n
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Missing a whole session at
#AAIC2023
because I forgot my badge at the hotel and they want to charge €100 to reprint it. You'd think a conference about Alzheimer's disease would be more sympathetic to memory lapses.
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I'm excited to share this short Review about AD pathological subtypes that
@OskarHansson9
and I put together for
@TrendsNeuro
. It's a short article but here's a quick thread summarizing it.
1/9
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I am supremely excited, humbled and honored to be Dr. Vogel! Thanks to
@pedrorosaneto
@alain_dagher
, Prof. Edith Hamel, Bill Seeley and
@IPNMcGill
for the amazing questions and conversations. And of course to
@acehigh1952
for putting up with me!!
@_JakeVogel_
did an AMAZING PhD defence presentation. So proud of him and the work he has done over the last 5 years. We will miss you in Montreal Jake!
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‼️ New paper alert ‼️
Interested in network spread or connectome-based modeling in AD? Check out our new paper in Nature Reviews Neuroscience:
Here's a quick thread summarizing the work:
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Timely given the current pandemic, we present epidemic spread of tau through the human brain. Instead of a virus traveling between cities using highways, we model tau traveling through brain regions using neuronal connections, in Alzheimer's disease 1/
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This is blowing my mind.. the hippocampus has an anterior and posterior blood supply, but some people don't have the anterior supply, and they are at increases risk for memory impairment. Thanks
@KonradWagstyl
for the share.
Hippocampal vascularization patterns vary between individuals. Perosa et al. show that a mixed hippocampal supply, as opposed to a single one, provides a hippocampal vascular reserve that protects against cognitive impairment.
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Interested in cognitive reserve and/or resilience? Our new paper (co-led with
@elman_jeremy
) argues that the one of the most popular methods for quantifying this concept, the residual method, contains some critical statistical limitations! 1/11
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‼️Postdoc opportunity‼️ Please RT 🙏
Are you interested in:
* Neurodegenerative disease
* Multi-omic analysis
* Machine learning/AI
* Neuroimaging
Come work with me and the whole BioFINDER team!
Apply here:
A quick thread about the position 👇
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‼️New preprint‼️
Disease progression modeling of:
* 3⃣ TDP-43 proteinopathies (ALS, FTLD-TDP, LATE-NC)
* Postmortem TDP-43 data from 22 🧠 regions
* N = 571 donors
We set out to create order from the progression patterns of these 3 proteinopathies? 1/13
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Short reference list limits are anachronisms that are bad for science. Am I missing something here? Is there a reason this is still in play? The 40 articles I need to remove from my accepted manuscript *all* deserve to be cited.
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‼️PhD positions available‼️ Please share/RT.
2⃣ PhD positions open in my lab!
Neuro/fMRI --
Quant. Biology/Omics --
Great data, great science, great team (
@biofinder_study
) and great fun. A quick thread about the positions: 1/5
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Secure first ever research grant at the PI level? Check! ✅
@lemwisse
and I will use AI to segment super-resolution slices of the medial temporal lobe.
We will soon open a postdoc position. Please reach out if you have AI skills and interest in AD or neuroanatomy!
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Hippocampus lovers harken! Check out our preprint, with
@relajoie
@BorisBernhardt
@evp82
@adp_diaz
@crocodoyle
+ others! An anterior-posterior gene expression gradient along the hippocampus is represented throughout the brain. 1/3
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Do you publish with ADNI data?
Journals often force you to add the monstrous author list to the end of your paper, with arbitrary affiliation numbering. I wouldn't wish this task on my worst enemies. Here is some code that will do it for you:
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If you're looking for a postdoc or are a prospective graduate student, I'll be recruiting trainees soon. If you're interested in aging/AD and any of:
* Multi-omics
* Machine learning / deep learning
* Neuroimaging / fMRI
Please do reach out, or come find me at
#AAIC2022
!
Big news!! I've decided to turn down (!) an NIH K99/R00 and instead take a tenure track position at
@lunduniversity
!! I will be opening my own lab by the end of this year, which will use machine learning and multi-omic and imaging data to study ADRD. 🎉🎉🎉
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I'm super honored and humbled to be recognized by my favorite conference in the world:
@HAIconference
! This community feels like a family and I just feel lucky to be a part of it. Looking forward to more great research in years to come.
Jacob Vogel (
@_JakeVogel_
) got the Young Investigator Award!!!! We'll deserved!
@HAIconference
#HAI2020
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I'm seeing a lot of postdoc ads but very few stating "workspace with windows and natural light". After spending 4 years in a dungeon, this is a perk that has become surprisingly high priority for me. If you got it, flaunt it!
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Our paper on fine staging of TDP-43 proteinopathies has been accepted to Brain and the uncorrected proofs are now available online:
See thread below for a summary of our findings.
‼️New preprint‼️
Disease progression modeling of:
* 3⃣ TDP-43 proteinopathies (ALS, FTLD-TDP, LATE-NC)
* Postmortem TDP-43 data from 22 🧠 regions
* N = 571 donors
We set out to create order from the progression patterns of these 3 proteinopathies? 1/13
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I am hiring a research technician to help process and analyze multimodal neuroimaging data. Please RT!!
* Great opportunity to gain research experience pre-PhD
* Access to exciting data
* Opportunities for independent projects
Apply here:
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‼️ Postdoc ad // Please RT/circulate ‼️
Are you interested in
* Big euroimaging and multi-omic data?
* Neurodegenerativ disease?
The
@biofinder_study
is looking for a talented postdoc to sink their teeth into some rare and exciting data!
Apply here:
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The preprint is out! We use diffusion models to show strong evidence of tau spreading through communicating neurons, even in normal aging. The process may then be accelerated by amyloid.
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‼️ Paper alert ‼️
Link:
Interested in psychedelics research? fMRI? In our new review we delve deep into this very hot topic.
While some exciting findings have emerged, the (very mixed) quality of research ended up as a big part of the story.
1/
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Can you make pediatric growth charts but for the human brain, and for the entire lifespan (age 0-100)? Here we tried just that with *over 100k T1 images*, deriving centile scores for normal brains as well as various diagnostic categories. Check it out!
“Brain charts for the human lifespan”! The result of 200 people putting their 🧠🧠🧠together (120,000+ of them!) to generate growth curves from mid-gestation to 100 years. &
@jakob_seidlitz
@SimonWhite83
@edbullmore
@Aaron_A_B
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By popular demand, we have now deposited the brain maps summarizing our AD tau-PET subtypes on Neurovault!
These include average SUVR, Tau Z, and difference images for each subtype
Thanks due to
@OskarHansson9
& multi-tau collaboration members!
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Proud of the Prevent-AD for going open access! A great resource of cognitive, imaging and fluid biomarker data in cognitively healthy older adults at risk for AD. Info in the new preprint!
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Are you interested in using SuStaIn () on your data? Next month we'll be debuting a persistent resource of video tutorials and hosting a live Q&A and type-along workshop! Sign up if you're interested: and please retweet!!
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I'm sure this has been said before but it bears repeating. Journals: why these restrictions to # of references? Consider:
a) There are way more papers out there than there used to be.
b) Multiple refs = more reliable finding
c) Majority readership is online: no space limitations
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Check out this preprint!!
Antemortem fMRI followed by postmortem synaptic morphology and proteomic measures. Supports the notion that molecular similarity underscores functional connectivity -- but within-subject!
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Hooray! Super excited to give an oral presention at
@OHBM
this summer, on behalf of a group of stellar collaborators:
A molecular gradient along the longitudinal axis of the human hippocampus informs brain function
See you at the Imaging Genetics session!
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I'm so lucky to have an amazing, inspiring PhD committee featuring
@pierre_bellec
,
@mallarchkrvrty1
and
@misicbata
and
@acehigh1952
. And yesterday, they allowed me to pass my thesis seminar, granting me permission to begin writing my thesis!! 🌠🌠🌠. Any advice before I jump in?
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This is incredible and heartening news. I applaud those involved, am super on board, and I even let myself dare to hope this will be the start of something more widespread!!
All NeuroImage and NeuroImage:Reports editors have resigned over the high publication fee, and are starting a new non-profit journal
This comes with great regret, and a huge amount of thought and discussion- please read announcement to get more details.
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This is one of the most impressive datasets I've seen. The ingenuity, care and detail with which this data was painstakingly curated and shared should be lauded. Amazing work to all involved!!
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Just got this email last night. Always nice to get messages from fans and admirers. Anyone else getting these emails, or should I consider this evidence I've finally made it?
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My grades were terrible, got kicked out of high-school, went to a college without grades. N=1 but.. about to have a PhD (🤞).. just saying
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Interesting paper -- replicates previous work showing BOLD hyperactivation in older adults (compared to young adults) during cognitive tasks, but no corresponding increase in glucose metabolism 🤔
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Can confirm!
This guy just got officially promoted to Full Professor of Molecular Medicine at
@goteborgsuni
🥳. Incredibly grateful to all my companions on the way here! Onwards and upwards, friends!!
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LOL just stumbled on this 2007 note describing a radiological signal deemed the "Puppy sign". LOVE the illustration, which basically is like "look how much this looks like a dog!"
Really curious to hear from you radiologists/neurologists if this is actually common terminology?
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Wow! So impressed by this paper from
@ytquiroz
's group! The paper shows robust changes in functional organization of the brains of people with genetic mutations causing AD. An important one for understanding links between 🧠 organization and cognition.
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Huge news!! Large longitudinal imaging and cognitive dataset of cognitive healthy older adults with a family history of Alzheimer's disease. Proud and in admiration of the Prevent-AD for making their data open!!!
The PREVENT-AD dataset is released open today!! 1704 MRI, 556 amyloid and tau CSF samples, blood markers, genetic info and longitudinal cognitive data on ~400 at risk individuals. Link to the open platform coming soon.
#openscience
#opendata
#neuroimaging
#CONP2019
@prevent_ad
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Fantastically delivered plenary talk by
@RikOssenkoppele
at day 1 of AAIC, really setting the tone!
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I'm really getting convinced by the sensitivity of these measures!
Spotorno et al. show that cortical mean diffusivity, a measure of cortical microstructure derived from diffusion MRI, is able to track disease progression on the AD continuum, and could thus be a promising outcome measure for clinical trials.
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p-tau217, you're the one
Janelidze et al. test 10 plasma phospho-tau assays head-to-head for their ability to detect abnormal brain amyloid-β status and predict future progression to Alzheimer's dementia in individuals with mild cognitive impairment.
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Great preprint showing "abnormal" tau pathology in temporal regions can precede amyloid deposition. This is shown in both pathology data at autopsy, and separately using PET and CSF data in vivo. Cool stuff from Leon,
@NeilOxtoby
, Alex et al!
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‼️ Postdoc opportunity ‼️
We're looking for someone with 💻 ~AI skills~ 🧠 to join the
@biofinder_study
team for an extremely cool project. As always, very rare data and exciting research questions!
Only open for another week!! Apply here:
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Pardon my french but I just stumbled on a shit ton of open psychometric data. Maybe ya'll already know about this, but, I was looking around for some real "human" data for a course I'm teaching and.. whelp, here's some:
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SuStaIn is an algorithm that allows simultaneous subtyping and staging of biomarker trajectories. SuStaIn can now be applied not just to continuous data, but also Ordinal data (e.g. visual ratings, pathology scores, Likert-scale items, etc:
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!!! Derivatives of DWI data for a diverse pediatric dataset (PING), processed using state-of-the-art pipeline! I've always found it hard to find derived DWI connectomes out there. Glad to see this data made available! Way to go bff
@noorigami
!!
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For anyone delving into the transcriptomics world, this is a must read. Amazing work by
@BenzingerNeuro1
et al!
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Literally the first floor of our Airbnb in Rome for the
@OHBM
hackathon. We're eating both on our terrasse. 😉
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Preprint lead by the amazing
@LevitisLiza
! Network diffusion models predict the spread of amyloid in LOAD and ADAD. A portion of ADAD subjects had a distinct striatal amyloid pattern and potentially a shorter disease course.
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This paper on tau replication vs. spreading has been circulating recently. It’s really cool and worth a read. But I don’t agree with a lot of the interpretations I’ve been seeing out there in the twittersphere. I’ll get into this below. 1/9
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Time to start figuring out the appropriate use criteria, because accurate blood tests for AD pathology are here.
❗️Publication❗️
Head-to-head comparison between a highly accurate plasma biomarker and FDA-approved and clinically used CSF biomarkers
🩸
#ptau217
is clinically comparable or superior to CSF biomarkers to detect
#Alzheimer
's pathologies
@NatureMedicine
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Yo AD Twitter community: who all is going to OHBM in Glasgow??
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Anyone interested in understanding neurodegenerative diseases beyond just grand averages (e.g. subtypes, copathology, variability) should check out this conference!!
The speaker list is 🔥🔥🔥🔥
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Thoughtful work by
@alexa_pichetb
@sylv_villeneuve
and
@evp82
et al. disentangling the impact of aging and AD on brain atrophy. AD and aging have additive effects on atrophy throughout the brain, however GM network disorganization specific to AD
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So excited to conduct research as a DDLS fellow, especially alongside the amazing
@consiglio_cr
! This is an impressive network built around cutting edge scientific principals. I feel lucky to be a part of it!
Welcome to the WCMM family
@consiglio_cr
and
@_JakeVogel_
! The SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS) is the latest initiative of the KAW foundation to create a national infrastructure for data-driven research in life sciences.
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At
#OHBM
and interested in hippocampus? ~*Gradients*~? All that plus gene expression? Come check out the Imaging Genetics session in the Choir room (not the Chair room!) at 10:30, or poster W325!
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What an incredible week in Paris for the Nilearn code sprint!! I merged my first ever PRs and learned more I'm a week than I probably have all year. Big thanks to
@GaelVaroquaux
and
@BertrandThirion
for hosting, and the rest of the amazing team!
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I'm gonna share a few threads about my first week playing with
#DALLE
2. First, a thread on some of the images that DALL-E 2 and I made together that impressed me the most:
"A venus landscape painted in the style of Manet"
1/n
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Such useful work. Wish this was around during my PhD. Had to learn many of these techniques through oral tradition 😅
🧠Neuroimaging peeps🧠 our field is blessed with beautiful visualizations. Our preprint provides 3 tools to help move toward code-based & replicable visualization:
📗practical guide (why should I?)
📦package selector (which one?)
🏗️code template generator (how do I start?)
👇🧵
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Certain psychoses seen to behave a lot like neurodegenerative diseases compared to other psychiatric disorders. Interesting work suggesting network based spread of brain atrophy in psychosis!
📈New & improved pre-print on the network-based spreading of grey matter changes across multiple stages of psychosis! We find that (1) 🧠volume changes are strongly constrained by axonal connections & (2) 🎯the hippocampus may be an epicenter of spread 1/n
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Could not be more excited about this one! The brainstem has seemed so inaccessible for so long. Biggupz to
@misicbata
,
@JustineYHansen
and collaborators for starting to chart the path!
Integrating brainstem and cortical functional architectures |
Led by
@JustineYHansen
400 cortical regions + 58 brainstem nuclei. Hit it 🎸🤘😎⤵️
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A fun project to be a part of and very exciting results! Huge congrats to the talented
@JustineYHansen
,
@misicbata
and the crew!
Mapping gene transcription and neurocognition across human neocortex |
led by
@JustineYHansen
w/
@rossdavism
@_JakeVogel_
@jakob_seidlitz
@danilobzdok
Can we identify molecular signatures of cognitive processes? Follow along!
@NatureHumBehav
⤵️
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It's been over a week since this happened. I'm still waiting for the same thing from other journals. If you're an editor and not working on the a similar protest.. what are you doing? This spark needs to start a fire!
All NeuroImage and NeuroImage:Reports editors have resigned over the high publication fee, and are starting a new non-profit journal
This comes with great regret, and a huge amount of thought and discussion- please read announcement to get more details.
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Wish I could say misconduct like this is rare but I don't think it is. But focusing on individual perpetrators probably misses the greater issue of a twisted incentive system and poor accountability that really drives this type of behavior.
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Such a well deserved accomplishment!! Can confirm both Alexa and Montreal are *amazing*!!
‼️ I will start as an Assistant Professor at the Aging Center
@criugm
@UMontreal
this fall 🧠🥳
I will be looking for students, postdocs, staff to build my group, do not hesitate to reach out!
Also happy to meet during
#AAIC24
in Philly!
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Python based ROI painter!!
Ending 2021 tired but a promise is a promise. Here it is🎁.
pip install ggseg==0.1
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Just gonna leave this here...
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This was one of the rare papers where I liked it even more after reading it closely. Here's a nice synopsis by Alzforum (as always) that I had the pleasure of commenting on. Great work from the Amsterdam team and to lead author
@EmmaCoomans
In pairs of identical twins, tau tangles accumulate in strikingly similar patterns, but stage of
#alzheimersdisease
and lifestyle can still make a difference.
@vuamsterdam
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A new open AD dataset with PET!! These are hard to come by. They are looking for people to help them share even more data, so please contact Sylvia. She is also *the best* person so guaranteed to be a good experience.
1/5 We are about to release the PREVENT-AD Stage 2 open dataset that will include PET, MEG, … and 5 yrs of additional cognitive FU. 🥳
@alexa_pichetb
@prevent_ad
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Sampling of tau staining and seeding across 25 brain regions in 20 individuals shows some fairly unexpected results that defy convention... and a lot of heterogeneity across individuals ;-)
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We shouldn't let this get swept away by the constantly changing news cycle. This is a premier data resource setting a dangerous precedent of pay to play. Not a policy conducive of a healthy scientific community.
Is anyone else annoyed that they've paid over £7,000 to access UK Biobank data, and now we have to also pay to analyse that data on the RAP?.....or am I just being a scrooge? I feel like being able to analyse the data *should* be included in the access fee?
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Super excited about this project!! This is the first time I've seen tau spread models actually forecasting future tau levels at the regional level. And the findings of phases of transport followed by production have potentially important implications for tau trials!
Thrilled to share a new preprint on regional tau modelling across the Alzheimer's continuum. A quick summary...
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This important paper has some really contentious implications. E.g.:
* Many previously reported associations between CSF biomarkers (e.g. between tau and inflammation) may be spurious.
* CSF A-T+ group -- maybe not a thing.
Must read for proteomics + CSF biomarker peeps.
🚨New preprint!!
Led by PhD student
@karlssonlinda1
, we reveal a confounding signal in CSF proteomics data and present a new method to address it! Our method results in better biomarkers and, without it, spurious findings can arise. Check out this thread👇
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Just saw this 2018 paper showing considerable AD pathology at autopsy in people under 40 living in heavily polluted conditions.
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This application closes this coming Tuesday, but there's still time to apply!
‼️PhD positions available‼️ Please share/RT.
2⃣ PhD positions open in my lab!
Neuro/fMRI --
Quant. Biology/Omics --
Great data, great science, great team (
@biofinder_study
) and great fun. A quick thread about the positions: 1/5
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Another modern classic by
@JustineYHansen
and
@misicbata
. Words cannot contain my enthusiasm for this one!!
Integrating multimodal and multiscale connectivity blueprints of the human cerebral cortex in health and disease |
Led by
@JustineYHansen
Brain networks hither and yon
@PLOSBiology
⤵️
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Sorry this isn't academic, but my band recently released a single and it's been getting some pretty good press. Check it out if you like loud music:
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One of the more interesting projects I've been a part of!! Subtypes of Lewy body neuropathology further support the idea that some people have predominant brain pathology while others experience more peripheral accumulation. Amazing work by ⭐
@SEMastenbroek
!!
‼️New preprint‼️
🔗Led by PhD student
@SEMastenbroek
, we unveil three different progression patterns of Lewy body pathology. Disease progression modeling of:
* Postmortem Lewy-type α-synuclein data from 10 🧠 regions
* N=814 donors
👇👇👇
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I'm really excited for this meeting -- anyone interested in modeling disease progression should consider checking it out!
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I really think "grease the poles" should replace the phrase "good news" in Philadelphia.
"Grease the poles, Wawa is having a sale on hoagies!"
"Grease the poles, I passed my candidacy exam!"
Go birds.
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Wow -- network changes preceding amyloid accumulation! But, kind of seems like the amyloid accumulators actually have preserved DMN connectivity/DMN segregation. Opposite of what one might expect?
Even before plaques develop, listless astrocytes allow neurons to work themselves into a frenzy. This places astrocytes earlier in the pathological cascade than expected.
@KU_Leuven
@ucl
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Very attractive job ad from Lund U looking for a researcher <5 years from terminal degree to start a research program in "data-driven Precision Medicine and Diagnostics". Plus you'd get to work alongside
@OskarHansson9
and
@biofinder_study
team! 👀👀👀
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Fascinating work by superhumans
@JustineYHansen
and
@misicbata
. Do network features or molecular features contribute most to disease pathology across disorders? This one really made me think! A must read!
Molecular and connectomic vulnerability shape cross-disorder cortical abnormalities |
by
@JustineYHansen
w/
@goliashf
@_JakeVogel_
@njahanshad
@PTenigma
@alain_dagher
Predicting cortical thinning in 13 diseases: molecular vs connectomic deathmatch!⤵️
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Important study showing neurovascular changes as measured with ASL occur quite late in the AD process, not early on as some previous literature has suggested. A challenge to the vascular hypothesis of AD?
Paper alert 🚨 Excited to share that our paper is out
@_JCBFM
. We show that ASL-CBF changes occur at later stages of AD and are correlated with tau, synaptic and axonal degeneration. Huge thanks to all the co-authors and
@biofinder_study
.
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"Advocates for approval said the need is desperate, while opponents say the drug -- priced at $56,000 a year -- would bring in billions for Biogen while failing to help patients." This is an issue. Much respect to Dr. Knopman for taking a stand!
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Finally, I’ll be opening my own lab at the end of this year. If you’re interested in this kind of work, especially as it relates to neurodegenerative disease, do reach out!
/end
If you're looking for a postdoc or are a prospective graduate student, I'll be recruiting trainees soon. If you're interested in aging/AD and any of:
* Multi-omics
* Machine learning / deep learning
* Neuroimaging / fMRI
Please do reach out, or come find me at
#AAIC2022
!
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If you're using BIDS (and you ought to be if you're organizing large datasets), you absolutely *must* try CuBIDS. It really saves a lot of time in what are otherwise often arduous data curation journeys.
We are thrilled to announce that our paper, "Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets," was just published in NeuroImage! 💻🧠
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Everyone stop exercising!! Just kidding, but interesting negative-ish finding from a big meta-analysis:
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