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When George W. Bush restricted national funding for stem cell research, the people of California passed a bond measure to fund stem cell research here. As a result, biotech exploded in the state, creating tens of thousands of jobs and generating billions. As a Californian, I want us to do the same with research Republicans are gutting now. Let's hire fired CDC scientists & make it the CCDC, the Calif Center for Disease Control & Prevention.

When George W. Bush restricted national funding for stem cell research, the people of California passed a bond measure to fund stem cell research here. As a result, biotech exploded in the state, creating tens of thousands of jobs and generating billions…

Headline that says mushrooms may talk to one another with up to 50 words

so they're mycoblogging

Seems like he could unbox it some more

Seriously though I wish everyone on the s4me forum extremely well, and I hope they can all have compassionate treatment and relief from their illnesses

Go aim a salami, I'm a nominative determinee

Preprint - COVID-19 Reproduction Numbers and Long COVID Prevalences in California State Prisons, 2024, Worden et al. COVID-19 Reproduction Numbers and Long COVID Prevalences in California State Prisons Lee Worden; Rae Wannier; Helena Archer; Seth Blumberg; Ada T Kwan;...

I'm a nominative determinism beneficiary now
www.s4me.info/threads/covi...

Kendrick Lamar during the Superbowl halftime show. He’s looking into the camera and smiling while saying “Say, Drake” while performing his song, Not Like Us.

Me greeting the developers of a platform on Zoom knowing I'm about to share a spreadsheet full of accessibility issues.

(A longer version of this thread was previously posted on Mastodon btw - length limits are stricter here)
mathstodon.xyz/@lworden/113...

JAN TAIT & THE BEAR YouTube video by Emily Doolittle

www.youtube.com/watch?v=XHzF...

Hi folks! Please follow and share so we can build the momentum necessary to turn the amazing medieval folktale Jan Tait and the Bear into an animated chamber opera, with music by @emilydooolittle.bsky.social, produced by Greenlight Creative.

Academic institutions in the US need to seriously consider how they will support and protect their minority faculty during this time. The conditions we face are already hostile for most - targeted attacks and added barriers to advancement will push many to simply walk away.

Thread about new preprint on dynamics and impacts of COVID-19 outbreaks in California state prisons
#PoliticalEpi #SocialEpi #PublicHealth #EpiSky #IDSky 😷 #RStats

Screenshot of text from the manuscript: “Between 1990 and 2009, CDCR was found in multiple court rulings to be providing inadequate medical care, inadequate medical screening of incoming prison residents, and untimely response to medical emergencies, as a result of overcrowding and underprovision of medical services. The U.S. Supreme Court upheld these rulings in 2011, found CDCR to be in violation of the Eighth Amendment to the U.S. Constitution, which prohibits cruel and unusual punishment, and ordered the population to be reduced. In 2020, as a result of the first San Quentin outbreak, the prison’s management was again found in violation of the Eighth Amendment, in ‘the worst epidemiological disaster in California correctional history,’ by failing to heed recommendations to reduce crowding by decarcerating a portion of the population. While the later ruling awaits appeal, holding incarcerated individuals in crowded buildings with inadequate protections and care while a deadly disease spreads from room to room continues to be cruel and unusual, and will be cruel and wrong even if it becomes usual.” [citations omitted from alt-text - see manuscript for citations and references]

Screenshot of text from manuscript [see manuscript for citations and references]: “While COVID-19 outbreaks in California state prisons have become fewer since early 2022, they have continued. Further outbreaks are likely, both of COVID-19, with possible loss of effectiveness of vaccination and natural immunity, and of other diseases, both old and new, potentially aggravated by the immune system damage associated with long COVID. We urge comprehensive medical care for all those suffering from ongoing effects of COVID-19 in the prisons, and decarceration to improve prevention of future outbreaks of the disease and of others that may emerge.”

Our prisons continue to be unsafe places where large future disease outbreaks are likely, and we urge decarceration to protect public health, and comprehensive medical care for those affected by COVID in the prisons.

Figure caption: Results from SQ [San Quentin State Prison]. A: Cases detected per day, with seven-day average. Starting date of each outbreak is marked by a vertical gray line. B: Positive and negative tests per day by building. Y-axis labels are building ID numbers. Buildings are grouped by facility. Scale bar at upper right gives number of tests. C: Estimated incidence by day by building, colored by room type. D: Incidence by room type and outbreak. E: Estimated effective R by day per building. F: Distribution of effective R in each room type. Features: Large outbreak of a bit over 2,000 cases in June/July 2020, as readers may remember. Largely concentrated to one facility of 5 buildings within the prison, containing cells with open door type. Reproduction numbers peaked between 1 and 2 in that outbreak. There was another outbreak of 500-600 cases in January 2022, mainly across two facilities comprised of Cell, Open and Dorm, Uncategorized, with reproduction numbers again peaking largely between 1 and 2, and a little over 2 as well in the dorms.

Figure caption: Results from ASP [Avenal State Prison]. (the rest of the caption is same as in SQ figure). Features: a long outbreak from May 2020 through January 2021, totaling about 2800 cases and affecting all 7 facilities (the internet says ASP has 6 facilities, but maybe they set up a field hospital or such and classified it as another one). Room/door types are mainly Dorms, with open or unclassified doors. A second, smaller outbreak in Dec 2021-Jan 2022 also reaches everywhere in the prison and hits about 900 people. Reproduction numbers reach occasionally above 3.

We provide an extensive supplement, which includes a full page figure for each of the 35 CDCR prisons, detailing the time course and R of all outbreaks through buildings, and the types of rooms and doors involved.

Screenshot of text from the manuscript: “Public health writing on racial disparities often references Ruth Wilson Gilmore’s formulation that racism, as an ongoing social institution, ‘is the state-sanctioned or extralegal production and exploitation of group-differentiated vulnerability to premature death.’ While it has general application, this definition comes from Gilmore’s historical analysis of the growth and overfilling of the California state prison system (Gilmore, 2007). Both incarceration and health disparities are important cases of institutional racism by this definition.” [Note: the citation refers to Gilmore's book, The Golden Gulag]

Screenshot of text from the manuscript: “It follows that the spread of the SARS-CoV-2 virus in the prisons has itself emerged as a new manifestation of institutional racism in California, as the pandemic, together with the legal and management decisions that led to the large CDCR outbreaks of 2020–22, resulted in group-differentiated exposure to death and disability. The lasting impact of these outbreaks embodied by the hundreds of Black and Indigenous Californians living with long COVID symptoms as a result of these outbreaks, many with ongoing disability as a result, is a second, ongoing, new manifestation of institutional racism. A similar dynamic is likely to have occurred in other states and countries.”

We connect these findings with the literature on institutional racism in public health and incarceration: these outbreaks are a new manifestation of institutional racism at the intersection of mass incarceration and public health.

Estimated distribution of ever having long COVID through March 25, 2022, in the CDCR system and in California. Features: Black cases are around 25% of the cases inside and around 6% outside; Indigenous cases are around 1.7% inside and 0.4% outside.

We estimate 9,000–10,000 prison residents developed long COVID, 1,700–2,000 with disability as a result. As with infection, Black and Indigenous communities in California were disproportionately impacted.

Distribution of estimated R values by room type. Heavy lines mark the median value and 95% central interval. Features: All include plenty of values from 1 to 2.5 and beyond, as well as between 0 and 1. Median values are: Cell, Open: about 1.2; Cell, Closed: about 1.4. Dorm, Open: about 1.3. Dorm, Closed: about 2.1. Both Cell and Dorm, with door type uncategorized: about 1.6.

Estimated total incidence by room type in each season. Features: The biggest numbers are in Cell, Closed, at 14,200 cases in Fall 2020 and 6,460 cases in Winter 2021-2022. However, there are plenty of cases in all seasons, for example 2,460 in the Cell, Open type in Summer 2020, and 3,940 in Dorm, Uncategorized in Summer 2020.

Screenshot of text from the manuscript: “The control methods used to protect the residents of these crowded, unsafe buildings clearly failed. In the absence of evidence to the contrary, and given the nature of congregate settings and high transmissibility of the virus, we assess that any measures short of decarceration of overcrowded prisons are unlikely to be effective at preventing extensive disease spread during a ubiquitous airborne pandemic.”

We use innovative methods to estimate reproduction numbers (“R”), examining outbreak control attempts that moved residents between rooms: no systematic improvement in cells over dorms, or rooms with solid vs air-permeable doors.

Figure caption: (A) Cumulative incidence rate of COVID-19 infections in each CDCR institution (gray), in CDCR overall (black), and in California (black, dashed, with 95% confidence interval), using IHME estimate of true incidence in California (including incarcerated populations). Vertical lines separate three “waves” of transmission. Excess cases in the CDCR system are seen in the first two waves. (B) Racial/ethnic distribution of COVID-19 infections in the CDCR system and estimated infections in California over all three waves. (C) Attack rate of outbreaks in the CDCR system and estimated attack rate in California, in first two waves. (D) Estimated excess cases in CDCR system relative to statewide population, by race/ethnicity, in the first two waves of outbreaks. Gradations of lightness on horizontal bars indicate mean and 95% confidence interval of estimate. Features: (A) is same as in the previous post. In (B) CDCR cases are about 25% Black while statewide only about 6% are, and about 1.3% Indigenous while statewide 0.4% are. In (C) the first two waves reached twice as many people per capita inside than outside. In (D) the excess cases per 10,000 statewide population are well above 20 for Black and Indigenous people and below 10 for everyone else.

Because of disparities in incarceration, more of the people infected are Black and Indigenous in the prisons. We estimate the excess cases associated with prison outbreaks: far more in those communities than in other communities.

Cumulative incidence rate of COVID-19 infections in each CDCR institution (gray), in CDCR overall (black), and in California (black, dashed, with 95% confidence interval), using IHME estimate of true incidence in California (including incarcerated populations). Vertical lines separate three “waves” of transmission. Excess cases in the CDCR system are seen in the first two waves. Features: The first wave goes until early October 2020; CDCR cases rise to about 1000 per 10,000, driven by a fraction of the institutions, while state cases are about 500 per 10,000. The second wave is until the end of March 2021, and involves all CDCR institutions. CDCR attack rate rises to about 3,500 per 10,000 and in the state about 1,500 per 10,000. In the third wave all institutions are involved again and CDCR attack rate ends up around 5,000 per 10,000, while the state goes to somewhere north of 11,000 per 10,000, which is an outrageous rise. The Omicron wave was definitely huge, but this estimate of true cases (it's the estimate published by IHME) has about 100% of people being infected in just 2 or 3 months, which seems high to me.

Prison residents were infected at higher rates than people in the rest of the state, aside from the Omicron surge, which was exceptional.

Cases detected by testing, by day (7-day average) by institution. The case numbers are plotted as variations in darkness of a brown bar across the plot for each institution. The upper limit is 125 cases per day. Dark colors near the upper limit are seen in summer 2020 at CVSP and SQ, in winter 2020-21 at LAC, CMC and PVSP, and in winter 2021-22 at NKSP, WSP, and FSP. Full institution names are in the paper and online - I might also post them in this thread, I'm not sure because it's so long

Outbreak sizes by institution. Outbreaks of size 3 or greater are shown (black), with institution population size as of March 20, 2020 for comparison (gray). Adapted and updated from figure 1 of (Parsons and Worden, 2021). Many institutions had outbreaks exceeding 1000 people and there were even more smaller ones.

Over 66,000 prison residents were infected, out of about 200,000 total. All 35 state prisons had multiple outbreaks, including many very large ones that affected thousands of people.

Some major points:
- Disease spread was extensive and control efforts were not effective
- Thousands of long COVID cases
- Disproportionate impact on Black and Indigenous people
- We should release a lot of people as a matter of public health

COVID-19 Reproduction Numbers and Long COVID Prevalences in California State Prisons Prisons have been hotspots for COVID-19 and likely an important driver of racial disparity in disease burden. From the first COVID-19 case detected through March 25, 2022, 66,684 of 196,652 residents ...

In time, the need to know about long COVID arising from all the outbreaks in prisons became clear. Here is our preprint addressing all these things!
“COVID-19 Reproduction Numbers and Long COVID Prevalences in California State Prisons”
www.medrxiv.org/content/10.1...

It turned out, to do that we would need more data than we had - we got the data a while after the outbreak. Along the way I noticed that the racial breakdown of prison cases was being reported in ways that didn't tell the full story about racial disparities.

New paper! 4+ years in the making, now preprinted. Here's a thread about it.
In June 2020 I was asked to help analyze the COVID-19 outbreak just starting in the San Quentin State Prison, to see if the disease was spreading faster in some buildings than others.

“Absolute idealism must be couched in irony in order to be taken seriously.”

Andrew Anglin, Founder of the Daily Stormer

This is what people like Beauchamp miss, despite the fact they are paid to write about antisemitism online. Trolling is not a sign of lack of belief, just the opposite.

THE meme of 2025 for me.

We have nothing but the highest regard for public health workers, be they in the community, at a university, or in a government role. Many of you can’t speak out. But please know, we support you and we will be fighting for you.

Home - ProMED - ProMED-mail ProMED is the largest publicly-available surveillance system conducting global reporting of infectious diseases outbreaks. Subscribe today.

The CDC’s Morbidity & Mortality Weekly Report (MMWR) have been frozen but you can still get outbreak alerts from ProMED. We suggest the weekly digests to preserve your mental health.

Or curved lines that arc a little to the side between the black dots

According to this article, they have ordered CDC/NCHS to stop releasing data. Make sure you've downloaded what you need, #EpiSky. Some of the executive orders affect variables in these datasets.