Long term lung damage from COVID infection (NYTimes)

This is a beautiful 3-D illustration of CT scan findings of COVID infection in the lungs, and the stories of the patients who survived, and now have changed lives as a result. Sobering, and illustrates, that even though our treatments and vaccines are excellent, we still have long term consequences for some with infection. Keep paying attention: Covid is not done with us.

From the NYTimes.com



The Pandemic Uncovered Ways to Speed Up Science (NYTimes)

Turns out, there are ways that science, with focused effort, can do good work, and quickly. Also, we should pay volunteer reviewers for medical journals!


This is a nice quick (3 minute read) of the ways Science can be done quickly and effectively, and points out some of the common friction points that we can eliminate in our journey. Thanks to the NYTimes for giving us perspective on what we’ve just lived through.

Secrets of “Covid Brain Fog” are starting to lift (Wired.com)


Image from Wired.com. Link to story above.

Precise Science

Instead of “Brain Fog” from Covid, we can now say “a loss of oligodendrocytes” and “microglial reactivity” are causes of decreased memory, cognitive sharpness and fatigue post Covid infection.

I love that our smart scientist colleagues are linking out to the chemotherapy and other viral research literature to find common threads and discover the basis for such puzzling syndromes.


I DON’T love the ongoing Covid infection numbers, the lack of masking, the decrease in vaccinations, as about 20 to 50% of all new Covid infections develop into forms of Long Covid, with Brain Fog being a long-term common symptom.

Even as the risk of hospitalizations fall with the latest Covid variant, the risk of Long Covid has not. We should all be concerned about this. Stay safe out there, colleagues. We need your brain power.

What is Paxlovid? (Wired). One of the better explanations of how this drug works against COVID

from npr.org


I found this to be timely and interesting.

As a physician, my advice (and what I continue to do now for myself, my patients, at this point in our Covid world):

  • Continue masking when indoors in public, mask off ok outdoors
  • I’m not eating at establishments indoors: I look for outdoor dining OR take out
  • Keep up with Covid vaccinations (I’m currently at 4 total, and likely will continue every 6-month boosters)
  • For patients with: diabetes, cancer, kidney disease, immune disorder, or over 65: Paxlovid within 5 days of onset of symptoms if test positive for Covid, with main purpose NOT to stop symptoms, but to avoid hospitalization and severe illness.

At UCHealth, we still have test positivity rates in the 20% and 30%, which is a major underestimate of the illness, since there is widespread availability of home Covid testing, none of which is reported publicly. We are still seeing a substantial number of hospitalizations with Covid illness. The pandemic is changing, but this thing isn’t over y’all.

Stay well out there.

The Pandemic, the Patient Portal and a Pachyderm: 2 years later @uchealth

How do you fit a curve to your theories? Come along as CT tries to convince you that he’s right…

Over the past 2 years, our lives have been topsy-turvy. Here’s my previous post from April 2020 on the percent of patients using our My Health Connection portal at the beginning of the pandemic.

To be clear, the graphs I’ll be showing today indicates the percent of patients being seen each month at UCHealth, across all of our hospitals and clinics, who have an active My Health Connection (our brand of MyChart) patient portal account.

The tail end of the curve in March 2020 showed a dramatic uptick. So, what happened since then? In that 2020 post, I showed the March uptick in Patient Portal signups, anticipating an ongoing bump in patients. We believe this was mainly (back then) about connecting with the doctor, learning about and using Video (Virtual) Visits to see the doctor/provider since we were in the process of shutting down in-person clinics due to the pandemic.

March 2020: patients on uchealth’s portal

Of course we know what happened next: an explosion of video visits (see previous post), then the availability of COVID testing, and later the availability of COVID vaccines, all of which were easier to request and obtain via the Portal.

In the graph below, we extend our original graph and add the months following March of 2020. I think we can agree that there was a steeper increase in patient portal signups below. Specifically the months between April 2020 to April to 2021, the curve looks different. And then, following April 2021, the curve appears to change again. How do we make sense of this?

Jan 2019 – Jan 2022 patients on the portal

One way to think about this to apply a logistic regression. I’m both too unskilled and also too lazy to attempt that. Here is my powerpoint-low-tech version, where I’ve simply pasted a line on top of the graph. Are you convinced? Do you agree that April 2020 to April 2021 shows a divergent signup rate, and that after April, the signup rate has returned to some sort of “inevitable baseline growth rate”?

Theory #1: the elephant and the boa

As an aside, the curve above actually looks like that brilliant drawing by The Little Prince of an elephant swallowed by a boa constructor. Thus, the pachyderm.

Okay, back to our pseudo-analysis. Here is an alternate set of lines: maybe we just accelerated our patient portal signup for a year, and then hit our theoretical maximum at 86% of the population in our region being on the portal and there is no one else coming in, after April 2021?

Theory #2: The plateau

Sure! That looks like a better fit, right?

OR, could it be that BOTH are the case, an immediate acceleration of patient portal signups in March/April 2020, sustained increase for the year that encompasses: video visits, COVID testing, COVID vaccines, THEN a leveling off of portal signups since then?

Theory #3: Fun with more lines

Another side observation: In the headlong rush for patients signing up for our online portal service, I’m personally finding more patients who “have an active portal account” who have not seen messages I’ve sent to them. I believe there is a growing fundamental problem here with several possible causes:

  • Patients who signed up for the portal because of Covid testing or vaccine, but who otherwise do not have interest in communicating online
  • Patients whose FAMILY MEMBER or FRIEND signed them up (maybe even with the friend’s email address) just to get a Covid test or vaccine or monoclonal treatment
  • Patients who have changed email addresses (we know from previous work before the pandemic that up to 20% of patients may not be reachable at their given email address the next year)

Three Stories

Three stories, three sets of arbitrarily drawn lines. I also know that our data scientists are skilled enough to be able to do the math to justify any of these power-point-line drawings.

CMIO’s take: Now that we are seeing a dramatic drop in cases from our Omicron surge, and our hospitals are down below 100% census for the first time in TWO YEARS, we can now sit back and do some armchair theorizing. And then plan for our next chapter. Which do YOU think it is? Let me know.

The pandemic, patient messages and phone calls: Octopus or Starfish?

Here we are 19+ months into the pandemic. Time to look at our (unvalidated) trends within our 12 hospital, 1000 clinic health system in Colorado.

Top (blue) line indicates outpatient visit volume monthly from Sept 2019 through Sept 2021. Over 2 years, we saw that dramatic dip in volume in March. That was followed by a gradual recovery and a 10% sustained increase in volume since then. We have added some clinics to our system in the meantime.

Magenta line indicates online messages. We started at 58,000 monthly messages in September 2019, and have sustained 180,000 messages in the most recent 3 months of 2021, a 3 fold increase in patient messaging. OK to ignore that weird peak in Mar 2021, related to a one time system broadcast. This is a real concern for provider workload.

Orange: Surprisingly, we also see an increase in telephone messages (triage-type phone calls): from 23,000 to 35,000, a 1.5 x increase. This means that online messages have NOT replaced phone calls since the onset of the pandemic. This could be related to the growth in percentage of our patients who now have a portal account (growth from 70% to 85% of our patients enrolled in a portal account, over 1.6 million accounts), as well as existing portal-using patients sending more requests and messages, wanting to avoid in-person visits.

Red: Additionally, Scheduled Phone Calls (non-existent prior to pandemic) are now at 5000 monthly messages, and

Green: video (virtual) visits went from nearly zero, up to a peak of 70,000 a month, then stabilizing at 23,000 monthly.

It is an interesting, evolving picture. We have not formally changed staffing or workflow to accommodate this change in message and visit volume, and it has resulted in a massive increase in inbasket messages for providers and staff, with concerns of an unmanageable burden and real risks of burnout for providers and clinical staff.

We believe that, at its root, patients want care, are more anxious about their health during a pandemic, want to avoid in-person visits, have learned about our online tools, and are unclear as to the best way to interact with us.

We could: improve our “front door” experience “Here is how best to contact and work with us”. We could improve our triaging of incoming messages to find the right location/time/place (online message, eVisit by messaging, online chat, scheduled phone call, virtual visit, urgent care, emergency department, other innovative approach).

We could ensure our teams know the best practice for: handling patient questions, prescription renewals, referral requests, outreach programs, remote monitoring, when to suggest video or phone visits, huddling in-person to replace unending back-and-forth messaging.


As a result, we are kicking off a major Inbasket redesign initiative. Although our inbasket settings were carefully considered and modified over the years since 2011 (our original Epic go live) with careful feedback from our physicians and informaticists, we still have opportunities:

Inbasket TECHNICAL changes:

  • Eliminating “messages > 12 months old”
  • Reducing the “FYI” and not-actionable messages
  • Auto-deleting some categories of messages after some period of time
  • Creating smartphrase responses to improve thoughtful responses to team mates and to patients
  • Streamlining the ‘response buttons’

Inbasket WORKFLOW changes:

  • Creating best-practice teamwork for “top of license” work
  • Considering innovation tools to “auto-reply” to common questions
  • Moving complex conversations away from portal messages to scheduled phone calls, virtual visits, in-person visits, urgent care as appropriate
  • Considering billing for complex portal messages with patient consent

Just like with Physician Burnout and Wellness in general, there is plenty of work for everyone in Inbasket improvement: there are at least 8 arms to this octopus. Even if we can just “hack off” some of the arms (hmm, perhaps not the best metaphor for healthcare), we can certainly reshape the octopus into something more manageable (a starfish?).


CMIO’s take? Is your inbasket an octopus or starfish, or some other marine animal entirely? It is time for a wholesale re-imagining of our messaging and communications with patients and with each other. What are you and your teams doing in this area? Let me know.

The most effective way to approach the vaccine-hesitant

From Haymarket marketing communications website MM+M


This is a 28 minute podcast. The crucial moment (for me) is about 12:30.

Of the all the psychologies and tactics to address various subpopulations of the vaccine hesitate (for pediatrics, for adults, for COVID in particular), ONE tactic was most effective across all these subpopulations, use of “confirmation bias” as a tactic.

If you’re in a conversation about the vaccine, leave aside all the data and arguments.

Often we see people trying to persuade by saying ‘OK, here are the facts. Here’s why you should get vaccinated,’ ” Braude said. “But this research says actually what you should ask is ‘OK, why would someone want to get vaccinated?’ and have them go through the process in their own words. That works much better than the persuasion techniques we see people trying to use.

It turns out that 20-44% of people who answered this question, who were asked to TAKE THE EMPATHIC STEP of putting themselves in the shoes of someone wanting to be vaccinated, and then having to describe the reasons why, ended up changing their mind and agreeing to get vaccinated.

Huh. I think I have never done that. Time to learn and use something new.

CMIO’s take? There are so many interesting facets of the human mind. Even amongst physicians and healthcare workers, we have a lot to learn about how humans think, and how we make decisions. We need to harness this for the public good. Who is with me?

Covid Vax Status, and Our Mental Health Status

We have a monthly Epic Provider Newsletter where we share system updates, and I send CMIO Update paragraph to my colleagues. Here is my update for this month:

With our next Epic system upgrade this week, Covid Vaccine status is now in the patient Storyboard! This is HUGE. It is now instantly visible when opening the chart, if/when the patient was vaccinated. This should help with rapid patient assessments and counseling, since the Covid-19 Pandemic Crisis now morphs into Covid-19 Ongoing Management. Possible Vaccine Statuses include:

  • Unknown (instead of ‘unvaccinated’ we know lots of vaccinations are not in our system; this prompts us to ask)
  • Dose 1 complete (if a 2 dose vaccine)
  • Dose 2 overdue (if late for second)
  • Vaccinated (XX date) if within last 2 weeks
  • Vaccinated

This is a nice improvement in our EHR.

IN PARALLEL, in discussions with colleagues this week, there is a sense that we are emerging from the pandemic. However, the prevalent emotion is not necessarily “relief”. Some say that they feel a sense of PTSD, or symptoms of exhaustion. In my mind, I feel like we have just finished running a sprint and are ready to stop and lie down.

BUT NO, there is no time take a break, it is time to resume the marathon of our regular healthcare jobs. 

We spent the last 15 months putting aside our burnout, putting aside our lives, and putting EVERYTHING into fighting this crisis, hoping to extinguish it.

Now, we put down our crisis tools, and look up and see … no end in sight. There is no way we are all collectively taking a year-long vacation, and our psyche’s are just realizing, now it is back to our regular, difficult jobs.

So, what is YOUR Covid Recovery Status on the grid below?

from: Responder Stress Continuum, via CU Anschutz Psychiatry presentation

We are starting to use this Stress Continuum Model to assess ourselves, and each other. More than ever, we need to take care of ourselves, and each other.

CMIO’s take? I hope all of you DO find a way to ‘take a break’. Although it is not a celebration, we SHOULD recognize that we stood on the front lines of an astounding moment in history. I am proud to have stood with all of you.

The Eppendorf, CRISPR, Covid, and my medicine origin story

This post is THREE THINGS. A personal origin story, a (brief) book review, and a connection to recent stories on Pfizer and Moderna Covid vaccines. And, when we’re done, it might even tie together!

Image above: Dr. NoFronta Lobe, Mad Scientist. No this is not me in the research lab; this is me, a kindergarten parent at Halloween

My Origin Story (I was a budding molecular biologist in 1985)

I was alone in the brightly-lit sterile-white research lab; having spent 20 hours on a long, multi-day experiment. It was nearly midnight on Saturday in 1985. I was a college junior majoring in molecular biology, with aspirations of a scientific research career. I was studying P4 bacteriophage, a virus that attacks E coli bacteria.

The work sequence, I could now perform by heart: inoculate, incubate, centrifuge, enzyme reaction, pipette (fancy eyedropper tool) into an Eppendorf tube (a tiny plastic tapered tube. From a Q-tip-loaded with a single bacterial colony, I had carefully grown a quart of bacterial culture, then sequentially purified my sample down to 20 drops of a pearlescent white DNA solution.

So: 20 hours for 20 precious drops. 

Eppendorf tube, Fisher Scientific

Exhausted and looking forward to heading home, I was on my last steps before overnight refrigeration, so as I held the open Eppendorf in my left hand and my pipette in the right, I randomly thought: “What time is it? Am I going to miss the last Orange Line train going home?”

So, I moved to look at my watch…

And since my watch is on my left wrist, the Eppendorf tube in my left hand did a 180…

And I watched as all the liquid ran out … and onto the floor. 

I looked at the upside down Eppendorf, and then down at the floor and the drops of liquid there, uncomprehending. 

*How… what… nnnnnNNNNNOOOOOOOOOOO!!!*

My late-night-fogged brain finally registered SHOCK, DENIAL, ANGER, BARGAINING. The lab was deserted, I deemed it safe to express myself:

“F$*&@! S!#%! D&$%!” I said, eloquently.

Desperate, I dropped down and started using the pipette to suck up DIRTY droplets of DNA extract from the floor and replace it into the Eppendorf. After a few minutes I had about 1/3 of the liquid, now brown-tinged, back in the tube. Resigned, I put the tube in the fridge. 

NO time to fret, no time to start over. Nothing else to do. I got on my jacket and faced the Boston winter, and jogged for the Orange Line stop. 

Once on board that last train, I started to sob. There was no way that soiled sample would be any good. This COMPLETELY SUCKED. 

And, I realized, I really did not want to be here. I realized: I could do the scientific work, but, unlike some colleagues who revelled in long hours in pursuit of new knowledge, I was despondent, not very good at this, and missed being around people. 

That was the night I decided that bench research was not for me. I had thought my calling was in pure science, but this DNA catastrophe taught me where I didn’t want to be. I needed Humanism AND Science. So, medical school it was. I’ve never looked back. 

Molecular Biology after 1985 (CRISPR!)

Thirty-five years later after my profanity-laced change of career, Walter Isaacson chronicles the recent successes of genetic research, including the discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and CAS9 (CRISPR ASsociated protein #9).

Book review rating? 5/5 stars.

In a nutshell: Jennifer Doudna and Emmanuelle Charpentier, and many others raced to understand these strange “repeating sequences” in DNA and mRNA, realizing that they were bacterial defenses against “phage” viruses.

In this work, they discovered that CRISPR-Cas9, an mRNA plus protein complex could identify attacking virus mRNA and SLICE IT UP, deactivating it. They realized that this ancient protein complex could be taught to identify ANY RNA or DNA. Gene editing, invented by bacteria as a survival mechanism a millenia ago, co-opted by humans. Precise genetic scissors.

I enjoy Isaacson’s writing style. Not only does he clearly explain the adrenaline rush of scientific discovery (and the delicate dance between scientific sharing versus the race against other labs to publish and claim credit), but also the technical details of how CRISPR works.

Isaacson writes about Doudna and the response to Covid-19. What is even more astonishing about Dr. Doudna, the bench researcher and lab leader at Berkeley, is that she had the socio-political skills to bring together 40 leading geneticists across the Bay Area to successfully set up a brain trust to develop Covid-19 testing and vaccine development. This team lays much of the groundwork of the accomplishments of this past year.

Drs. Doudna and Charpentier were, deservedly, awarded the 2020 Nobel Prize in Biology “for the development of a method for genome editing.”

A personal note: my brief journey in molecular biology never quite crosses Dr. Doudna’s path, but I recognize the genetic tools mentioned, and studied the work of the luminaries in the field. I feel like a distant cousin to these scientists.

Highly recommended read, to understand the genetic foundation of our modern age.

Molecular Biology: the Covid fight

Here are 2 stories about Covid Vaccines, from the New York Times and WIRED.com, fascinating glimpses into the genomic-industrial complex. As of May 14th 2021, 36% of US adults are vaccinated against Covid-19. It is highly likely that these speedier and more effective mRNA-based detection tests and vaccines will forever be part of our lives. This could shorten development and improve accuracy of future vaccines.

WIRED.com story on Moderna’s Covid Vaccine trials


CMIO’s take? Our modern world is built from advances in scientific method, computing and now genome editing. Despite my early failure in the lab, I feel fortunate, in the field of medical informatics, to be close to all 3.

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