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Kamil Slowikowski @slowkow.com · 7d

A visualization of average resting heart rate in Germany from 2020 through 2022.

Link: corona-datenspende.github.io/en/vitaldata...

Data: zenodo.org/records/8229...

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Kamil Slowikowski @slowkow.com · 16d

A huge thank you to my coauthor Pritha Sen, mentor Chloe Villani, colleague Chris Cosgriff, and the whole COVID-19 Severity team for making this study possible and supporting me all these years. I am very grateful to the hundreds of people who created this opportunity to study disease severity.

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Kamil Slowikowski @slowkow.com · 16d

While many immunologic abnormalities in acute severe COVID-19 resolve during convalescence 3-months post-infection, we observed persistently high ICOS expression in regulatory T cells, potentially linking acute infection to chronic post-COVID syndromes.

**M.** Volcano plot for convalescent CD4 T cell subset 6 (Treg).
Dots indicate genes, x-axis indicates fold-change, y-axis indicates negative log10 p-value from multivariate linear regression.
Red color indicates FDR < 5%.

**N.** Box plot of *ICOS* gene expression in CD4 T cell subset 6 (Treg) in the convalescent data.
Fold-change and p-value is shown.
Dots represent patients, box plots indicate median and interquartile range, x-axis and hue represent convalescent COVID infection.

**O.** Box plot of *ICOS* gene expression in CD4 T cell subset 13 (Treg) in the acute data.
Dots represent patients, box plots indicate median and interquartile range, x-axis represents time point, and hue represents COVID infection.

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Kamil Slowikowski @slowkow.com · 16d

We also identify HLA-DQB1 amino acid positions associated with:
- COVID-19 disease severity
- specific TCRs in CD8 T cells
- viral load
- neutralization capacity of serum

**E.** Amino acid position associations with COVID severity for HLA-DQB1.
x-axis indicates position along the gene.
y-axis indicates negative log10 p-value from multivariate linear regression.
Black color indicates FDR < 5%.

**F.** Coefficients from the multivariate linear regression for the effect size of each amino acid position on COVID severity.
Amino acid positions D57 and V57 are highlighted.
Error bars indicate 95% CI.

**G.** Bar plots of the number of patients with each genotype.
Facets indicate genotype (0, 1, 2) for amino acid position D57 (top) and V57 (bottom).
x-axis indicates number of patients.
Hue indicates COVID severity.

**H.** Box plot of abundance of CD8 T cells with TRBV28, x-axis indicates time point and hue indicates genotype of HLA-DQB1 V57 (0, 1, 2).
P-value from multivariate linear regression.

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Kamil Slowikowski @slowkow.com · 16d

We found that tocilizumab eliminates CLU-expressing MDSCs and ISG-positive myeloid subsets, restores antigen presentation, and reactivates productive adaptive immunity.

In myeloid cells, the mRNA signature of tocilizumab treatment appears inverse to the signature of disease severity.

A scatter plot where each point represents a gene. The x-axis represents the fold-change of the gene in acute patients who received tocilizumab treatment, where genes induced after treatment are seen on the right and genes repressed after treatment are seen on the left. The y-axis represents the fold-change of the gene in acute patients, where genes associated with worse severity are seen on the top, and genes associated with lesser severity are seeon on the bottom. Some genes are labeled.

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Kamil Slowikowski @slowkow.com · 16d

Severe disease is also linked to autoantibodies targeting type I interferons, influenced by specific HLA-DQB1 allelic variants, and strongly correlated with serum IL-6 levels.

Here is a schematic representation of our findings:

A schematic that shows some factors associated with the severity of COVID-19. Starting with SARS-CoV-2 infection, the adaptive immune response should lead to successful elimination and convalescence. In some patients, various factors such as viral titer, age, autoantibodies, lymphopenia, serum IL-6 levels, TCR and BCR clones, and HLA genotypes can increase risk for severe disease. This leads to a feedback loop wherein lack of viral clearance leads to increased tissue damage. This is associated with myeloid cell dysfunction marked by impaired antigen presentation, which drives a non-productive adaptive immune response, as reflected by reduced expression of B and T cell gene programs involved in antigen recognition, immune synapse formation, and cytotoxicity. The anti-IL-6R antibody, tocilizumab, appears to reverse the mRNA signature of disease severity in myeloid cells.

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Kamil Slowikowski @slowkow.com · 16d

Our findings show that myeloid dysfunction, which is marked by impaired antigen presentation, drives a non-productive adaptive immune response, as reflected by reduced expression of B and T cell gene programs involved in antigen recognition, immune synapse formation, and cytotoxicity.

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Kamil Slowikowski @slowkow.com · 16d

We analyzed 2.5 million immune cells from 428 patients in three contemporaneous SARS-CoV-2 cohorts:
(1) acutely infected patients across severity levels and time points
(2) patients from a trial to study tocilizumab for COVID-19
(3) convalescent patients three months after infection

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Kamil Slowikowski @slowkow.com · 16d

I'd like to announce the medRxiv preprint of our latest work:

A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity.

www.medrxiv.org/content/10.1...

Overview of a research study about COVID-19. The study includes three cohorts: (1) 351 acute COVID-19 patients across 5 severity levels and 3 time points profiled by multiple modalities, (2) 4 acute COVID-19 patients treated with tocilizumab, (3) 73 patients, 43 of whom were previously infected with SARS-CoV-2 3 months ago. The overview shows the general study design and visualizations of the single-cell RNA sequencing data analyzed in this study.

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Kamil Slowikowski @slowkow.com · 25d

Search #Pubmed and view the results on a 2D embedding. Each point represents a paper, and similar papers are near each other. Colors indicate clusters of similar papers.

By Viktor Petukhov

github.com/multicore-ca...

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Reposted by Kamil Slowikowski

Iris van Rooij 💭 @irisvanrooij.bsky.social · Aug 12

AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...

AI slop and the destruction of knowledge

This week I was looking for info on what cognitive scientists mean when they speak of ‘domain-general’ cognition. I was curious, because the nuances are relevant for something I am researching at t…

irisvanrooijcogsci.com

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Kamil Slowikowski @slowkow.com · Aug 8

1. Make an Excel file with your author information
2. Drag and drop
3. Copy a nicely formatted author list into Word

🐶 slowkow.com/authorbud

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Kamil Slowikowski @slowkow.com · Aug 5

"After adjusting for smoking and other risk factors, we observed statistically significant and robust associations between air pollution and mortality."

"Air pollution was positively associated with death from lung cancer and cardiopulmonary disease"

pubmed.ncbi.nlm.nih.gov/8179653/

A graph from a 1993 article published in the New England Journal of Medicine illustrating the relationship between air pollution and mortality rates in six U.S. cities. The x-axis represents the concentration of fine particles (µg/m³), while the y-axis shows the adjusted mortality-rate ratios. Cities such as Steubenville, OH, and Portage, WI, are marked. The adjusted mortality rate for the most polluted of the cities (Steubenville, OH) is 1.26 times higher than the morality rate least polluted city (Portage, WI). Data from Dockery et al., NEJM 1993.

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Kamil Slowikowski @slowkow.com · Jul 16

Convert Markdown to C++, Python, MATLAB, and LaTeX

iheartla.github.io

by Yong Li

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Kamil Slowikowski @slowkow.com · Jul 15

Could you please share the original links or files for the source data you are using in these figures?

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Reposted by Kamil Slowikowski

Stand Up for Science! @standupforscience.bsky.social · May 14

☀️THE SUMMER FIGHT FOR SCIENCE☀️

🫵 WHO: You + all our friends

🧪 WHAT: Share science with your neighbors and tell them about the impact of proposed budget cuts.

🇺🇸 WHERE: Your local community

🏖️ WHEN: Now to Sept 30th

🔬 WHY: The 9/30 budget vote will determine the future of science in America.

The summer fight for science. The time is now. Join the fight at standupforscience.net.

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Kamil Slowikowski @slowkow.com · Jul 4

Thank you for sharing! Your work is inspiring.

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Reposted by Kamil Slowikowski

Alex Rubinsteyn @alexr.bsky.social · Jun 4

5 pages of this in the HHS Terminated Grants document

Link: taggs.hhs.gov/Content/Data...

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Reposted by Kamil Slowikowski

BK. Titanji @boghuma.bsky.social · Jun 4

The destruction of the medical research enterprise in the U.S. will go down in history as one of the most damaging choices a government has made in setting its population backwards
www.nytimes.com/interactive/...

Here Are the Nearly 2,500 Medical Research Grants Canceled or Delayed by Trump (Gift Article)

Some cuts have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye.

www.nytimes.com

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Reposted by Kamil Slowikowski

Michael Baym @baym.lol · May 13

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

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Reposted by Kamil Slowikowski

Senator Bernie Sanders @sanders.senate.gov · Apr 30

Illegal arrests made by the Trump administration are intended to spread fear and silence dissent.

We cannot allow Trump and his cronies to turn the United States of America into an authoritarian society in which people can be disappeared for their political beliefs.

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Reposted by Kamil Slowikowski

Representative Becca Balint @balint.house.gov · Apr 16

My colleagues and I demand answers from Kristi Noem and Marco Rubio about the illegal and inhumane abduction of Mohsen Mahdawi, a permanent legal resident of the United States.

The Constitution guarantees people within our borders basic rights, including due process and free speech.

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Reposted by Kamil Slowikowski

Representative Becca Balint @balint.house.gov · Apr 16

Kilmar Abrego Garcia must be released and brought home to Maryland. He is innocent. No government can snatch people off the street and ship them to prison without due process. It should terrify us all.

I'm thankful @vanhollen.senate.gov is headed there to demand his release.

Senator Chris Van Hollen @vanhollen.senate.gov · Apr 16

I just landed in San Salvador a little while ago, and I look forward to meeting with the team at the U.S. embassy to discuss the release of Mr. Abrego Garcia.

I also hope to meet with Salvadoran officials and with Kilmar himself. He was illegally abducted and needs to come home.

Just landed in El Salvador to discuss release of Kilmar Abrego Garcia

YouTube video by Senator Chris Van Hollen

youtube.com

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Reposted by Kamil Slowikowski

Democracy Now! @democracynow.org · Apr 16

"It is critically important that we as Americans, regardless of party, stand up for all of these students who are being detained," says Vermont's @balint.house.gov. "This has got to stop. This is Trump creating his own army of brownshirts right here in our country."

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Kamil Slowikowski @slowkow.com · Apr 9

Today, I watch with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted dismantling by the current administration.

American science is the envy of the world, but this global leadership is now threatened by draconian cuts to federal support of biomedical research through the defunding of grants and drastic reductions in funding for essential research costs and infrastructure.

This will have catastrophic consequences for the US biomedical research and medical sector, choking off the next generation of medical advances and undermining our global competitiveness at a time when other countries are working hard to overtake us.

— Ardem Patapoutian, Nobel laureate

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