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Rich Abdill

@richabdill.com
853 followers 1.2K following 102 posts

Bioinformatics, open data and meta-research at Sage Bionetworks

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Reposted by Rich Abdill
Vaughn Cooper @vscooper.micropopbio.org · 23/09/2026
Fantastic, comprehensive, useful review if you care about RNA modifications in bacteria: @asm.org @csdetweiler.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews
SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modificat...
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Rich Abdill @richabdill.com · 17/09/2026
I'm up much too early to be figuring out if this is just fun with computers or if CRISPR editors are going to get designed differently
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Rich Abdill @richabdill.com · 14/07/2026
New Sequence Read Archive standards, you have until next year to start uploading files with (checks notes) data in them ncbiinsights.ncbi.nlm.nih.gov/2026/06/29/s...
5. Sequence file content requirements 

To be accepted, each read file must: 

Contain at least one valid read—Empty files or files with no valid reads will be rejected 
Contain no empty reads—Files containing empty or incomplete reads will be rejected 
Include per-base quality scores—FASTQ and BAM/CRAM must contain standard quality information for all bases and reads 
Use valid IUPAC nucleotide codes—Allowed characters include:
A, C, G, T, U, R, Y, S, W, K, M, B, D, H, V, and N. Files may be flagged or rejected if >50% of bases are ambiguous 
Reference valid INSDC assemblies—If aligned, the reads must reference a publicly available INSDC assembly. If using a private or unreleased reference, submit as unaligned  
File should not be previously deposited—Duplicate submissions are not permitted; reference the existing accession instead
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Rich Abdill @richabdill.com · 07/07/2026
Just noticed Positron uses the Elastic License, and using MIT for some of the heavy components seems like a thoughtful approach. It would be interesting to get a legal perspective on how shops like Posit (and Elastic!) are balancing OSS with keeping the lights on positron.posit.co/licensing.html
positron.posit.co
Licensing – Positron
Positron is licensed under Elastic License 2.0, a source-available license. Free for personal, academic, and commercial use with minimal restrictions.
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Reposted by Rich Abdill
Crystal Fleming クリスタル @alwaystheself.bsky.social · 17/06/2026
He kept coming back, repeatedly (in the way AI often loops) to this idea of AI (specifically Claude) representing "a position without an address", and it became increasingly clear to me that there was some odd mystification happening. Of course LLM products have an address. It's a corporate address.
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Journal of Open Source Software @joss-openjournals.bsky.social · 05/05/2026
🎉 JOSS turns 10 today! Ten years, 3,500+ papers, 11,000+ authors, 4000+ reviewers, and a community that built something remarkable together. Thank you to everyone who's reviewed, edited, authored, or cheered us on along the way 💚 joss.theoj.org #openscience #opensource
joss.theoj.org
Journal of Open Source Software
Journal of Open Source Software (JOSS) is a developer friendly, open access journal for research software packages.
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Rich Abdill @richabdill.com · 02/05/2026
Shared memory for R objects. This will make bioinformatics work so, so much faster. If you have a script that uses multiple threads but is limited by the amount of memory required for each thread, this might be just a drop-in replacement that opens up every core opensource.posit.co/blog/2026-04...
opensource.posit.co
mori: Shared memory for R objects
mori is a new R package for sharing R objects across processes via OS-level shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same physical pages — share once, read anywhere.
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Reposted by Rich Abdill
Rachel Hall-Clifford, PhD, MPH, MSc @rahallclifford.bsky.social · 27/03/2026
This could be a game changer!! Diarrhea is global health's least sexy challenge, but it remains a top killer of children. E.coli is present in 98% of water sources in Guatemala, for example, and systematic water purification is incredibly challenging for low-resourced contexts.
clinicaltrialsarena.com
Oral vaccine cuts up to 80.6% of E.coli-triggered diarrhoea cases
The oral ETEC vaccine will now enter a pivotal Phase III trial across different countries and populations.
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Jeremy Berg @jeremymberg.bsky.social · 19/03/2026
OMB has posted the full-year apportionments for NIH. openomb.org/file/11511545 I believe this means that NIH now has the spending authority to fund grants! There may be nuances and I will be tracking these as best I can.
openomb.org
National Library of Medicine and 24 other accounts | 11511545
Apportionment file 11511545 (National Library of Medicine and 24 other accounts) retrieved from OMB public records
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ProPublica @propublica.org · 19/03/2026
As ProPublica journalists, we share a common purpose with inspectors general: to hold our government accountable by identifying waste, fraud and abuse. If you work in or have recently left the office of an inspector general, we want to hear from you.
propublica.org
An Open Letter to the Inspectors General Community
If you work in or have recently left the office of a federal inspector general, we need your insights to do important journalism.
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Colin Carlson @colincarlson.bsky.social · 17/03/2026
(unless you work on climate change or racial disparities or LGBTQ health or…)
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Drug Monkey @drugmonkey.bsky.social · 13/03/2026
“The leftover money from those terminations went to the US Treasury, not back to NIH.”
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Rich Abdill @richabdill.com · 12/03/2026
I don't have any insight into what the actual story is with the change to NIH data management plan requirements, but this clarification sounds like "We asked for lots of details, turns out we don't care" grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-26-046: Updated Elements of an NIH Data Management and Sharing Plan
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Updated Elements of an NIH Data Management and Sharing Plan NOT-OD-26-046. NIH
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Rich Abdill @richabdill.com · 03/03/2026
I was just talking about this the other day, 404 Media has been doing an incredible job laying out the threats posed by data brokers www.404media.co/cbp-tapped-i...
404media.co
CBP Tapped Into the Online Advertising Ecosystem To Track Peoples’ Movements
An internal DHS document obtained by 404 Media shows for the first time CBP used location data sourced from the online advertising industry to track phone locations. ICE has bought access to similar t...
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Rich Abdill @richabdill.com · 23/02/2026
Quick paper highlights a fun twist on methods transparency and reporting—even thorough descriptions may be interpretable only to humans. Interesting to consider using standardized syntax ("n=") for LLMs rather than older "semantic web" techniques www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Sample Size Reporting in Human Cancer Microbiome Research is Inconsistent and Unstandardized
Transparent and standardized sample size reporting is essential for reproducibility in microbiome research, and for enabling AI-driven data aggregation tools. This is of particular importance with reg...
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Reposted by Rich Abdill
Dan Garisto @dangaristo.bsky.social · 20/02/2026
😑
106. To flag grants for their DEI involvement, Fox entered the following
command into ChatGPT: “Does the following relate at all to DEI? Respond factually
in less than 120 characters. Begin with ‘Yes.’ or ‘No.’ followed by a brief explanation.
Do not use ‘this initiative’ or ‘this description’ in your response.” He then inserted
short descriptions of each grant. Fox did nothing to understand ChatGPT’s
interpretation of “DEI” as used in the command or to ensure that ChatGPT’s
interpretation of “DEI” matched his own.
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Nandita Garud @nanditagarud.bsky.social · 12/02/2026
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
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Reposted by Rich Abdill
Joe Robertson @joro.bsky.social · 12/02/2026
More than 400 people, including hundreds of citizens, were “sorted” at gun point into racial and ethnic groups by 200 ICE agents who fired flash-bang grenades into cars with people inside, pointed guns at children & demanded their zip tied parents not comfort them. apple.news/Ausdx6kWtT0e...
apple.news
Idaho families sue over immigration raid that swept up hundreds, including U.S. citizens — NBC News
About 400 people, including children and U.S. citizens, were detained for four hours while they were denied food and water in the raid, according to the lawsuit.
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Justin Hendrix @justinhendrix.bsky.social · 30/01/2026
A Minnesota woman observing ICE agents in her car was cornered on one-way streets. An agent approached, called her by name—citing facial recognition. Days later, her Global Entry and TSA privileges were revoked, with no explanation.
nytimes.com
How ICE Already Knows Who Minneapolis Protesters Are
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Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 29/01/2026
ICE's decision to just leave cars abandoned in the roads is one of those dystopian things that makes you recoil in shock when you encounter it.
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Rich Abdill @richabdill.com · 27/01/2026
What Americans Lose If Their National Center for Atmospheric Research Is Dismantled
eos.org
What Americans Lose If Their National Center for Atmospheric Research Is Dismantled - Eos
Five ways dismantling NCAR will cost the American people, and two ways to save it.
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CJ Ciaramella @cjciaramella.bsky.social · 23/01/2026
"We have a nice little database. Now you're considered a domestic terrorist." www.reddit.com/r/Maine/comm...
reddit.com
From the Maine community on Reddit: ICE tells legal observer she is a domestic terrorist for peacefully filming
Explore this post and more from the Maine community
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Rich Abdill @richabdill.com · 20/01/2026
Google's browser is now cutting off its own ads for eating up too many resources
Screenshot of a banner ad at the top of a website. It's been replaced by a dark box labeled "This ad used too many resources for your device, so chrome removed it."
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Jeremy Faust, MD @jeremyfaust.bsky.social · 15/01/2026
We have the CDC-funded Hepatitis Vaccine trial in Guinea-Bissau protocol. It’s worse than you thought. Check it out, first in Inside Medicine… with @pauloffit.bsky.social David Boulware and others. insidemedicine.substack.com/p/scoop-the-...
insidemedicine.substack.com
Scoop: The leaked protocol of the CDC-funded Hepatitis B vaccine trial in Guinea-Bissau. “This is another Tuskegee.”
The protocol reveals that the trial will withhold the Hepatitis B birth dose from thousands—without placebos, without universal maternal screening, and with endpoints critics call indefensible.
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UChicagoBSD @uchicagobsd.bsky.social · 12/01/2026
New research from @uchicagobsd.bsky.social shows that microbes in breast milk actually populate the infant gut, laying the foundation for a healthy microbiome. biologicalsciences.uchicago.edu/news/microbe... #ScienceNews #Microbiome #GutHealth
biologicalsciences.uchicago.edu
Microbes in breast milk help populate infant gut microbiomes
New study provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to infants’ gut microbiomes.
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Kat Abughazaleh @katmabu.bsky.social · 08/01/2026
You and your wife drop your 6-year-old off at school. You just moved here. You see ICE terrorizing your new neighbors. You film them, as is your legal right. Your wife complies with orders. She is then shot in the head. You still have to pick up your child later today. This could be you.
Distraught woman says ICE killed her wife in video after deadly Minneapolis shooting
"They killed my wife," the distraught woman says, adding, "They shot her in the head."
An ICE agent shot and killed a 37-year-old woman who was driving an SUV in Minneapolis on Wednesday. / Screenshot/@Breaking911"They killed my wife. I don't know what to do," the woman says through sobs in the footage, with a damaged SUV visible in the distance behind her. "We stopped to videotape, and they shot her in the head," the woman cries.
"We have a six-year-old at school," she says, almost unable to breathe, as a chaotic scene in which federal officers prevented at least one doctor who was on the scene from assisting the shot victim unfolds. "We're new here," the distraught woman says in despair.
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Eric Michael Garcia @ericmgarcia.bsky.social · 08/01/2026
Minneapolis public schools canceled classes officials after Roosevelt High School said armed Border Patrol officers came on school property during dismissal Wednesday and began tackling people, handcuffed two staff members and released chemical weapons on bystanders www.mprnews.org/story/2026/0...
mprnews.org
Minneapolis schools cancel classes after Border Patrol clash disrupts dismissal at Roosevelt
Minneapolis schools closed for the week citing safety concerns after an encounter involving armed Border Patrol agents near Roosevelt High School.
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Radley Balko @radleybalko.bsky.social · 08/01/2026
According to my sources, the FBI was initially open to a concurrent investigation with the MN Bureau of Criminal Apprehension (the state agency that would do this investigation). Trumpy U.S. Attorney Daniel Rosen heard about this and intervened, barring the FBI from cooperating with local police.
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Aaron Rupar @atrupar.com · 08/01/2026
Posts may be a bit more sporadic from me today as my kids are home from school because my city is being brutalized by the federal government to the extent that it's unsafe for schools to be open
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Aram Shabanian @aramshabanian.bsky.social · 08/01/2026
via Minneapolis photographer Chris Juhn on Facebook
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Carl T. Bergstrom @carlbergstrom.com · 02/01/2026
"I don’t know why my fellowship was terminated. I suspect that it has something to do with studying a species that doesn’t fit the binary of what we expect to see in nature, with completely different males and females." @carlzimmer.com profiles my wonderful coauthor @jjinsing.bsky.social Gift link.
nytimes.com
He Studied Why Some Female Birds Look Like Males
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Jess Calarco @jessicacalarco.com · 23/12/2025
The point was never to save money. That was only ever a convenient justification for an effort to decimate the public sector and dismantle the US social safety net.
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Chase Madar @madar.bsky.social · 23/12/2025
Really sick victim-blaming. Sick, sick shit www.nytimes.com/2025/12/22/u...
nytimes.com
Trump Administration Will Investigate Brown’s Security After Shooting
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 18/12/2025
This is the best piece I’ve read so far on why the Guinea-Bissau RCT, in which a proven life-saving vaccine will be deliberately WITHHELD, is unethical “When benefit is established, withholding an intervention is no longer neutral experimentation it becomes premeditated harm”
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 19/12/2025
I was interviewed for @theguardian.com by the wonderful @melodyschreiber.com, one of the finest health reporters in the world, about what I called a “neocolonialist” study planned by Danish researchers in Guinea-Bissau, funded by RFK Jr. So many red flags 🚩🚩🚩🚩🚩🚩🚩 www.theguardian.com/society/2025...
theguardian.com
US plan for $1.6m hepatitis B vaccine study in Africa called ‘highly unethical’
Experts decry ‘neocolonialist’ Guinea-Bissau study after Trump administration changed advice for US babies
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Stacey Burns @wentrogue.bsky.social · 09/12/2025
“She has marks on her neck and wrist from where agents restrained her. Agents cut off her wedding ring and held her in leg shackles at Whipple Federal Building for about five hours.” Her crime: witnessing ICE, from a distance.
mprnews.org
Federal agents arrest citizen observer watching ICE detain neighbors on her north Minneapolis block
Susan Tincher, a 55-year-old American citizen, appears to be the first observer arrested by federal immigration enforcement officers since the agency launched an immigration surge in the Twin Cities l...
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anil oza @aniloza.bsky.social · 08/12/2025
“The only reason I don’t have this funding is because my last name is Rodriguez.” MOSAIC checked many of the boxes of the administration — but that didn't matter. It was terminated, and left grantees scrambling Next installment of American Science, Shattered: www.statnews.com/2025/12/08/t...
statnews.com
NIH shut out hundreds of young scientists from funding to start their own labs
Special Report: The NIH has shut out hundreds of young scientists from funding to start their own labs.
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Jason Koebler @jasonkoebler.bsky.social · 08/12/2025
404 Media is making a print zine! About the surveillance technologies used by ICE. 16 pages, riso printed. Shipping early January. Features reworked versions of our best reporting and a few new things. We're very excited! And hope to do more if people like it: www.404media.co/404-media-is...
404media.co
404 Media Is Making a Zine
We are publishing a risograph-printed zine about the surveillance technologies used by ICE.
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 04/12/2025
Absolutely unconscionable: Dr Prasad won't share details, data, evidence, or proof of causality. We just have Dr Tracy Beth Høeg's vibes - that's the assessment. AND: "FDA vaccine staff disagreed with the assessment that the reported deaths were caused by vaccines" endpoints.news/fda-says-it-...
endpoints.news
FDA says it won't release details of claimed Covid vaccine deaths in 'near term'
Details from an investigation by CBER Director Vinay Prasad into 10 alleged child deaths related to Covid-19 vaccines won't be coming soon, an FDA spokesperson told Endpoints News on Wednesday.
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Alejandra Caraballo @esqueer.net · 04/12/2025
48 years. That's how long trans women have been eligible to compete in tennis.
A screenshot of a 1977 newspaper article titled “Renee Richards Ruled Eligible for U.S. Open” by Neil Amdur. The article reports that Dr. Renee Richards won a court ruling allowing her to compete in the U.S. Open without taking a sex chromosome test. It describes a State Supreme Court justice’s decision declaring the test requirement discriminatory and blocking tennis associations from excluding her.
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Dave Levitan @davelevitan.bsky.social · 02/12/2025
The former oil executive/DOE official who held the all-staff meeting announcing the change repeatedly told the scientists who work on clean energy that she "hates" clean energy.
gravityisgone.com
'A Collective WTF': National Renewable Energy Laboratory Gets a Trumpian Name Change
NREL employees, many of whom joined the lab specifically to work toward its clean energy mission, are not happy about the oil-soaked leadership's moves.
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Dr. Jens Foell @jensfoell.de · 29/11/2025
Read through this and think about how absolutely unimaginable a message like this would have been just 13 months ago. The suppression of US academic liberty has been accepted and normalized instantly. The federal government is in full control of what thoughts and values are allowed in lecture halls
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Radley Balko @radleybalko.bsky.social · 20/11/2025
They lied about it. All of it. A thug cop shot an unarmed woman five times without justification, boasted about it to his colleagues, and then this administration tried cover it all up by arresting her and charging her with felonies.
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Dan Diamond @ddiamond.bsky.social · 20/11/2025
CDC has overhauled its website to assert that “the claim ‘vaccines do not cause autism’ is not an evidence-based claim”
Autism and
Vaccines
QUESTIONS AND CONCERNS
PAGE 2 OF 9 | ALL PAGES J
For Everyone
NOV. 19, 2025
KEY POINTS
• The claim "vaccines do not cause autism" is not an evidence-based claim because studies have not ruled out the possibility that infant vaccines cause autism.
• Studies supporting a link have been ignored by health authorities.HHS Research on Plausible Biologic
Mechanisms between Vaccines and Autism
HHS will evaluate plausible biologic mechanisms between early childhood vaccinations and autism. Mechanisms for further investigation include the impacts of aluminum adjuvants, risks for certain children with mitochondrial disorders, harms of neuroinflammation, and more.
* The header "Vaccines do not cause autism" has not been removed due to an agreement with the chair of the
U.S. Senate Health, Education, Labor, and Pensions Committee that it would remain on the CDC website.
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Arjun Raj @arjunraj.bsky.social · 15/11/2025
Also, here’s an accessible video intro:
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Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 13/11/2025
NEW: @propublica.org investigated the Chicago apartment raid where kids were zip-tied and citizens detained for hours. They find: - NONE of the arrested were criminally charged - NO evidence the building was "filled with TdA terrorists." - ZERO legitimate reason for DHS to rappel from a Blackhawk.
As a Black Hawk helicopter roared overhead, the slender, 28-year-old immigrant from Venezuela answered softly, his eyes darting to a television crew invited to film the raid. Next to Caicedo, masked Border Patrol agents inspected another man’s tattoos and asked him if he belonged to Tren de Aragua, the Venezuelan gang that the Trump administration has designated a terrorist group.

Until that moment, Caicedo’s only interaction with law enforcement in his two-and-a-half years in the United States had been a traffic stop two weeks earlier for driving without a license or insurance, according to the records we reviewed. Chicago police had run a background check on him and found no prior arrests, no warrants and no evidence that he was in a gang. Caicedo said he had a pending asylum application, a steady job at a taco joint and a girlfriend whose daughter attended elementary school across the street. 

None of that mattered. The U.S. government paraded him and his neighbors in front of the cameras and called their arrests a spectacular victory against terrorism. But later, after the cameras had gone, prosecutors didn’t charge Caicedo with a crime. They didn’t accuse him of being a terrorist. And after a brief hearing in immigration court, the government sent him back to the country he had fled nine years earlier.

“I lost everything,” he said in a phone interview from his mother’s home in the Venezuelan city of Valencia. “For those fools, everyone from Venezuela is a criminal.”
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Jonathan Howard @joho.bsky.social · 12/11/2025
Prasad and Hoeg are censoring studies showing the covid vaccine is safe. More great reporting by @lizzylawrence.bsky.social www.statnews.com/2025/11/12/f...
statnews.com
How two top FDA officials are quietly upending vaccine regulations
Vinay Prasad and Tracy Beth Høeg mix skepticism with new ways to define risk in pursuing sweeping changes to vaccine policy at the FDA.
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Rich Abdill @richabdill.com · 06/11/2025
Looks like @moderation.bsky.app automatically mutes "rude" content? What an embarrassingly infantalizing thing for a social media platform to do
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Scott Horton @robertscotthorton.bsky.social · 04/11/2025
From Bovino's deposition: (1) he calls protestors "violent" if they articulate views hostile to ICE, even if no violence is manifested; (2) he instructs his forces to attack and arrest protestors who express "hyperbolic comments," which is to say, criticism of ICE and Bovino.
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Dare Obasanjo @carnage4life.bsky.social · 01/11/2025
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review. This is due to being overwhelmed by a hundreds of AI generated papers a month. Yet another open submission process killed by LLMs.
blog.arxiv.org
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
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