Tag Archives: microbiology

Lo Is Domestic AF: Homemade Sauerkraut FAIL

This year we joined a CSA to support the local economy and are likely to continue doing so moving forward. We received cabbage in one of our weekly shares, so we decided to use Joshua Weissman’s recipe for sauerkraut. His recipe is not to blame. I take all the blame on this one. Jacob says he wants to take some of it too.

Unfortunately, this did not go as planned. Three days in everything seemed okay. We extended to the full seven days. Maybe that’s where we went wrong.

First, we lifted the bags full of water off the top of the cabbage. Immediately, something wasn’t right. I have a very sensitive nose. Jacob really had to shove his face in there to get a good whiff. He refused to allow me to take a picture of his reaction, so I agreed to put my face in it so he could get a truly emotive video.

I smelled rotten, vomit inducing cabbage for all of you. I hope you’re happy. No. I did not eat it. 🦆 🤢 🤮

I hate wasting food, but I want to learn how to make these things. I will do full troubleshooting later, but I think I will use more pH based microbial selection for lactobacillus in the future. That means buying litmus paper and doing daily testing, plus adjusting the pH using vinegar.

You may have noticed that we had two jars. That’s because I wanted red pepper flakes in one of the batches. I can’t say anything for what this did because they both smelled so bad.

In other news: we’re out of risotto rice, so there’s been a delay in making our pesto risotto, but we have made another new batch of vegan pesto. I can post that recipe next. Additionally, we have a lot more of those chocolate chip cookie mixes for us to doctor with random things. I would love to hear suggestions!

If you enjoyed this, please like, comment, and/or share this post. I would love to hear what strange ingredients you want to try mixing into chocolate chip cookies. Turmeric might be a good one 🤔

Thank you for reading. I hope everyone has a wonder weekend and a beautiful summer solstice ☀️🌈🌞

Recovery: If 1 million Americans get coronavirus, what will the recovery look like?

Success With Flattening the Curve

I posted this on twitter last night after the briefing.

Remember how we were projected to have 2.5 Million cases? We have reduced the projected number of infected Americans by 1.5 Million to only 1 Million. 1 Million is not great, but that’s a big change. That is called flattening the curve and everyone should be thinking that is really amazing (I know I am). They did not mention the number in the briefing (frustratingly). But forecasting has gotten a bad rep in the past.

For those who are math nerds – that’s a linear fit to 1,000,000 (switch from exponential), which some dude in the early 20th century proposed was when the growth in the number of reported influenza cases was hitting it’s predictable rounded peak forecasted the maximum cumulative cases (the limit). I’ve been trying to go through my notes to remember more about how this all works because I don’t remember the name of who came up with all of this and I’m trying to find the paper. I will update this and replace this rambling text when I do.

Recovery in the US

Recovery is not a guarantee that you will not get SARS-CoV-2 again. There are recorded cases of reinfection internationally. We do not have enough data to know if this is reactivation of latent virus or if this is true reinfection. That said, we are finally looking for asymptomatic, both recovered and not, individuals.

A vaccine would be able to address this by using adjuvants designed to induce helper T cell immunity in addition to antibody based immunity. Vaccines take time. Realistically a good vaccine will be on the market in March 2021 at the absolute earliest. Anything before that and I will be floored if it has sufficient efficacy to help.

In New York City, 40-50% of patients experiencing severe acute respiratory distress will be placed on a ventilator. If recovery required a ventilator, the testimonies from survivors do not suggest a population able to return to the workforce tomorrow. Shortness of breath, weakness, and other long term effects of hypoxia threaten the be permanent disabilities in this portion of the population.

But what if you do have immunity? You’ll be able to test that. What if you’re one of the lucky ones? I guess that’s up to you.

We’re in this together.

source:https://coronavirus.1point3acres.com/en

At each of these state clusters there is at least one urban center that has the dominant reservoir population. Once movement between urban centers (New York -> Chicago -> Houston -> Miami -> Atlanta -> Boston -> Dallas -> L.A. -> San Francisco -> Chicago -> Orlando -> Pittsburgh -> (etc. etc. etc.)) stops then there will no longer be additions of infected individuals into the populations. This is why non-essential planes need to be grounded.

I live in Montana. I am so blessed. I want to make it clear that we still need to behave. It only takes 1 person to infect 10.

My family and people I love live in Washington, Idaho, Oregon, Montana, California, Texas, Alabama, Louisiana, Florida, Virginia, New York, New Jersey, Massachusetts, New Mexico, Arizona and Maine. I’m terrified for everyone.

We’re going to gradually come to a new normal. Ask me questions and I’ll eventually address them in updates on these original posts.

As a change of pace, I’m going to stop writing about the coronavirus for a while unless there’s something people specifically think of graphs or other things that would be useful questions to be answered in something new instead of an update. I still have a backlog of a couple posts that will still get done though.

I will be starting to write short stories and weird little memoir style posts so people can enjoy my writing separate from the reviews.

Thank you for reading. Without you this is a shout into the void.

Is the US flattening the curve? Yes. Significantly? Who knows.

How do you describe that feeling of watching numbers climb and realizing that you’re watching in real time the most global example of what you’ve studied and taught your entire adult life?

Dread? Excitement? Existence?

When teaching about pandemics we teach students to look retrospectively at the numbers of those that have recovered versus those that have died. We make estimates on the numbers of those that were actually infected based on documentation available (or more recently – on documented confirmation). At about 6:00PM on 27 March 2020 twice as many people had died of covid-19 in the United States as have recovered. Seeing those numbers broke my heart for a moment, so I had to talk it out to myself somewhere.

https://coronavirus.1point3acres.com/en as of 6:26 PM MST 27 March 2020

It’s too early to call what it will look like in the United States in terms of our final numbers with covid-19. At this time these numbers are skewed by post-mortem testing and testing criteria that limits test accessibility to those already in need of medical intervention over home care.

Things might look scary, but don’t give up hope. Update 30 March 2020: and reporting started coming in of recoveries! Part of why this reporting may have been delayed is due to stringent testing criteria.

https://coronavirus.1point3acres.com/en as of 12:47 AM MST 30 March 2020. The criteria most are going by: 2 negative covid-19 swabs with a minimum of 24 hours separation.

The reason for this standard is that there is a very high false negative rate with the rt-PCR based test. If anything goes wrong along the way – say there’s a bad reagent, too low of a sample of viral particles, or something goes wrong that invalidates the test it will come back negative. This is the bane of every graduate student that has ever done rt-PCR. They will tell you their horror stories, especially if they were from poorly funded labs.

For some additional hope.

There’s this amazing power of graphs. We can look at growth of reported cases overtime to project the number of cumulative reported cases in the United States in the future.

I started keeping these to track the projection if we stayed on an exponential number of cases reported (aware of typo – did not plan on using this graph for anything originally)

Even as we have expanded albeit limited testing across the United States the overall rate of growth of total cumulative cases is slowing. While this hope is based on very limited data, could it be that we may actually be flattening the curve?

Equation is changing – are we flattening? I’m not sure. We added a zero. [Does some math]. I don’t know if that’s significant yet.

We’re able to see the slope change as the day to day numbers change. Thus, we can see when our efforts are working. (See below)

Source: https://coronavirus.1point3acres.com/en has the ability to build graphs showing how the US has slowed growth from 28% to 25%. That 3% isn’t much, but it’s something.
Source https://coronavirus.1point3acres.com/en But remember that our reporting is primarily coming from one place right now. Go to the website and visit this graph – it’s actually a movie!

This is part of why we need accurate reporting above anything else. The numbers that only require home care matter. In order to accurately understanding the danger of a disease we have to know how many people have it and are acting as asymptomatic or low symptomatic carriers. This influences anticipatory healthcare planning decisions for patients and facilities. I will address this a bit more later in regards to the limitations of cultural understanding around death, dying, and disease.

Update 30 March 2020: Exciting New Graph! If we start looking at the growth in the number of reported cases since improved surveillance across the United States started around March 19th – Yes, the US is kind of flattening the curve. But not enough. We’re also not far enough in to predict the peak.

We can be hopeful. As of 30 March 2020 we were set to diagnose our 500,000th case on 4 April, 2020. Flattening the curve is succeeding in different parts of the country. I will be addressing this in a new post. As a brief update as of 12:01AM 1 April, 2020, we have moved that projection out to 5 April, 2020. My model is limited by not knowing what the current daily max testing capacity of the United States is yet.

Update 5 April 2020:

Hey, look! We didn’t hit 500,000 cases. That’s incredibly comforting and is a fantastic sign. That said, we still have a backlog of COVID-19 tests, an untested positive population acting as a reservoir to continue infecting our healthy population, and we have no control over this. At this point, it is believed that SARS-CoV-2 will become a seasonal illness in the United States.

Source: Same as before

Remember how I said before that the 500,000th case had been pushed out to 5th April? Now, that’s 6th April, 2020 if only looking at the cumulative cases since the 15,000th case in the United States. What if we look at since 23 March? On this day we had approximately 46,000 confirmed cases, with the next day climbing to 55,000 confirmed cases. This is the date we should look at to consider since 50,000 cases reported.

Source: same as before

It’s not changing. There’s enough growth in of confirmed cases in parts of the country that any flattening is being overwhelmed right now. America’s current check up isn’t doing so hot.

A website for further seeing how your area is doing with flattening the curve. It is grading the United States with a D, and I agree.

PPE Shortages

It’s not the fault of our healthcare workers and everyone needs to show gratitude. The United States is facing extreme PPE shortages, resulting in healthcare workers being put at risk for infection and at risk for being vectors of covid-19. Hospital acquired infections have long been a problem in the US due to poor hygiene practices among staff and invasive devices used in hospital settings such as catheters, PICC lines, and IVs. While this has been combatted over recent years by the installation of improved educational programs and the implementation of disease control specialist positions in hospitals and clinics, these measures are useless without sufficient PPE. Washing hands and hand sanitization does only so much. We dedicate a lot of research time and money to this topic.

Diagnostic Testing Has Barriers

Point of Care rapid testing is a luxury afforded us over the past ten years (and toward the end of the 20th century) for strep throat, influenza, drug screenings, and other common “ailments” that bring you in to say hello to someone like me (only using quotes because I included drug screenings). The fact that we have this soon to be available for the coronavirus at all is incredible. Not only will this help with disease surveillance, but we have the ability to accurately study a pandemic in real time on a scale like never before. We could have the ability to intervene and institute true quarantine measures assuming we roll out extensive Point of Care screening for everyone.

But until then, can I even trust this data?

Rituals Around Disease, Death & Dying Complicate Things

How many people are dying at home untested? Remember that across America we have incredibly diverse customs about death and dying.

I recently spoke with friends in New York City and she mentioned that she knew members of certain cultural communities that though they were symptomatic were not getting tested. Part of why this happens is because of cultural beliefs around illness and dying. It’s going to be scary and everyone is reacting in ways that may deter them from getting tested. This will limit our surveillance and will also result in transmission within communities.

In the American South (where I’m from) families conduct home hospice even during severe illness out of pride and the cost of healthcare. Once the family member has died they will contact the local mortician. While it might no longer be legal to do home embalming and many states have prevented home burials, this has never stopped families from caring for the dead. Caring for the ones we love as a final act is one of the most essential acts as a family member that is often robbed of Americans elsewhere across the United States. In twenty to fifty years will we need to do go all paleovirology/anthrovirology (actual fields!) on disinterred bodies to get the actual numbers? Or will we go the route of China with incinerating covid-19 presumed bodies without testing? Will we go the route of the US during 1918? Will we burn it all?

Another thing to consider with any pandemic is how the rituals around death in the home contribute to the spread of a disease. This paper regarding the Ebola pandemic addresses why it is important to understand how we culturally handle death in times of pandemic in order to appropriately control spread.

Future Questions We Will Hopefully Answer:

As we look into ways to protect our healthcare workers with limited PPE we should be reminded that there are other ways we control the spread of disease.

Are healthcare workers on PReP faring better?

Many of the antivirals in PReP and PeP are being tested in the treatment of covid-19. Healthcare workers in Emergency Medicine have recently started turning to PReP and PeP to prevent the spread of HIV as a result of blood born pathogen exposure. Are these healthcare workers faring better than those not on PReP? Only time will tell since the number of workers on PReP reporting is still rather low.

What percent of the population needs to participate in social distancing in order to flatten the curve?

There’s isn’t actually an exact percent. What’s critical is that those at highest risk of being effective vectors for covid-19 during the transmission period of infection while shedding virus are able to infect as few other people as possible. This is a complicated question I’ve broken down into a couple parts.

Who actually needs to be on a stay-at-home order / essential workers only order for us to flatten the curve?

Go Fill Out Your Damn Census So I Have A Better Map

On the U.S. Census map above population density is shown in dark areas. Are you in that darker half? Stay. The 🦆 Home unless you are an essential worker.

Are you NOT in the darker half? Then you should be worried if you hear that there’s community transmission in your county. At that point practice social-distancing.

But you’re not out of the woods yet my friends. I have some more criteria for you:

How far away does your closest neighbor live? If you live in an apartment building – you should stay home. Live out in the country? Congratulations you lucky son of a gun! We’ve shown those city slickers that living in the underserved parts of America with crappy, dying economies that have been sputtering out and suffering at the hands of a global economy and evil corporations ain’t so bad, now is it? Or is it.

How far away is the closest interstate, highway, airport, train station, and other means of connection? Ever go to the gas station close to those things? May want to rethink that. Those are going to be your highest risk areas.

There’s a certain percentage of the population that can’t participate in the Stay at Home orders. It’s not their faults and they should be treated with the utmost kindness. They are taking huge risks. If you are a member of this population there are ways to assess how high risk your workplace is (if you’re interested). The actions of everyone else helps to make up for that by creating distance and reducing the number of people available for transmission at all. I know that’s a little messed up, but that is part of the theory behind it.

Source: https://www.census.gov/library/visualizations/interactive/2014-2018-median-age-by-county.html#

What is the median age of your area? Serious question though. Also, how old are you? Yes, this disease is affecting young people and those with conditions that make them more vulnerable. But I want you think about what kind of threat you are posing to the other people in your area by being a vector. If you live in a dark blue area, even if there hasn’t been a reported case in your county yet – staying home or social distancing is protecting this vulnerable population. You don’t want to have helped transmit the first.

source: https://www.unacast.com/covid19/social-distancing-scoreboard

(Update 5 April 2020) What Is Your Social Distancing Score?

You have thought about population density. You have thought about your median age group and how that plays into susceptibility of your area. The actions of those around you also put you at risk. In the flattening the curve check ups on New York, Pennsylvania, and New Jersey I talk about how important social distancing is right now and how big of an impact it is going to have on what we see in the future, such as the one vs. two peaks in New Jersey. But remember that not everywhere can social distance. Pay attention to the areas graded “F” as we address poverty below and in this post here.

Source: https://www.census.gov/library/visualizations/2019/comm/family-gatherings.html Do you live in a multigenerational household or live close by to family and see each other often?

Do you live in a multigenerational household or live close by to family? Do you see them often?

You absolutely need to be trying to stay home. These stay at home orders are critical to you. Illnesses like this can spread through families like wildfire. We love our families, right? Keep our families safe. If you are an essential business employee, it is even more important that you protect your family and isolate from them if possible. In many cases there is caregiving. This is addressed more in this post.

Source: https://www.census.gov/library/visualizations/interactive/2014-2018-poverty-rate-by-county.html#

Do you live in an area that is severely impoverished?

I hate asking this question because it is loaded. Click here for further reading on an additional opinion regarding race and healthcare inequality relating to poverty. Problems with the wealth and resource gaps in America demonstrates the huge gap between the way we treat people and I’m from a deep blue dot on the Chesapeake Bay where those resources aren’t available.

Disease outbreaks are worse in areas where poverty is not appropriately addressed. If you live in an area like this, you need to take stay at home orders seriously and the problem is, you can’t. And it’s not your fault. Our government and humanity are failing you.

I made a new post to address this more. Point is: stay home if you can, but be compassionate with yourself if you can’t.

What is determined to be essential and how do they determine what percentage of the workforce can be considered essential?

Oh. See, here’s the fun part. They don’t. They think of essential services, not the total number of employees this prevents from participating in social distancing. The state governments will figure out why this is really really dumb pretty fast, especially since many are now seeing hiring booms in those fields (like gas stations and weed delivery). I’m not an economist or a business person. People need to eat. This will be a strain on efforts that has to be monitored.

If people are interested in hearing me rant about the topics I’m actually an “expert” (by degrees and academic research/teaching background only) in let me know. If you are I’ll actually go back and edit this rant and dress it up a bit.

Thank you to anyone reading this. Without you this is just a shout into the ether.