Sunday, April 12, 2020
Sentinel surveillance for COVID-19: nasal swabs of teachers, service workers, gym coaches and healthcare workers
I have been wondering about how we'd do surveillance when we move away from our current stay-at-home condition. Assuming we use self-administered nasal swabs rather than obnoxious nasopharyngeal swaps we could distribute volumes of mail-in test kits (goal of 24h turnaround) to school teachers, healthcare workers, gym coaches, bartenders, and so on. Volunteers would swab weekly, mail in kit with their bar code on them.
We'd need a few million kits per week to do this.
Happily, this is discussed in the April 7 paper by McClellan, Gottlie, et al. I'd heard of the paper, I just needed to read it.
So I don't need to worry ... it's taken care of.
Saturday, April 04, 2020
It's just the flu
So how does COVID-19 compare to the spectrum of influenza? Wikipedia has an article on the CDC pandemic severity index that ranks various influenza pandemics. The 1918 pandemic was Category 5 - a case fatality rate (CFR) of 2.0% or higher. The worst influenza in my life was the Hong Kong flu with a CFR below 0.5%. It is said to have killed a million people worldwide (out of 3 billion).
The COVID-10 CFR seems to fit that range. We think its CFR is somewhere between 0.7% (based on presumed cases) and 1.5% (based on excess mortality). So by CFR it is arguably "just the flu".
What about if we look at the other half of the equation - the Basic reproduction number (R0 how contagious a disease is)? Wikipedia is again helpful; influenza ranges from 0.9 to 2.8, the early estimates for COVID-19 the 1.4 to 3.9. So COVID-19 fits the influenza model there as well, as long as we include monster events that cause historic devastation.
We can also look at who dies, and the disability of those who survive. Some influenza takes the young, some take the middle-aged, most take the old. COVID-19 seems to go for the middle-aged and old, so again flu like. As to disability, I haven't seen any reports on post-influenza disability. I wonder if persistent lung damage will be one way that COVID-19 is not flu like. We don't know yet.
So, yeah, COVID-19 mostly fits within the spectrum of influenza, as long as we include pandemics that hit every 100 years or so. It's "just the flu," in the same sense that WW I was "just a war".
Tuesday, March 17, 2020
Hydroxychloroquine, COVID-19, and Lupus
Both chloroquine and hydroxychloroquine inhibit SARS-CoV-2 in vitro, although hydroxychloroquine appears to have more potent antiviral activity [75].I think saw a post somewhere that claimed it interferes with viral replication inside infected lung tissue but I can't find it now.
That's obviously great if it works out.
If it does work out though, it might be worth looking again at old (and still current) ideas that rheumatic disorders that response to hydroxychloroquine (esp. SLE, RA) are infectious in origin. Maybe an RNA virus ...
Sunday, March 15, 2020
Exercise and sanity in the time of you-know-what
- Trail, road, gravel biking. Extreme aerosol diffusion. Antiviral ultraviolet radiation built in. Social distance built in. Definite good. Buy your gravel bike now before they're all gone, but any road bike will do. Start commuting by bike.
- Mountain biking. Same, but different bike.
- Running. Hard to be less social. Trail runs nicer. For St Paul MN -- Battle Creek!
- Garage Gym. Get that car out of there. Who cares about cars anyway? Bench, bar, weights, programming from your local CrossFit franchise. Get some friends together at a distance (byob).
- Your local CrossFit ... class sizes will be smallish. Open the big doors and spread outside where the air flow is amazing. Dress for the occasion. Learn to love open air deadlift and those $!$^@ runs and rows and such.
- Golf. Chase (Tim) wants this. Lots of social distance! Don't share clubs :-).
- Lake swimming. Cold in MN March, but eventually ...
- Inline Skating! Time for a comeback. Get those blades out of the attic. Airflow, etc. Join the Facebook Minnesota Inline Skate Club Group.
- Hiking. Slow trail running for the win.
- Rock climbing outdoors. Sweat and blood do not transmit. Maybe don't spit on the rope?
- Paddling! Canoe, Kayak -- air flow, social distancing, perfect.
- Fishing -- not much exercise, but good for sanity.
- Tennis -- don't spit on the ball.
- Free fishing licenses!
- Waive state park fees.
Friday, March 13, 2020
COVID-03 and COVID-19: influenza co-infection and multiple strains
The entire SARS story puzzles the heck out of me. Why did so many nurses die, even in locations that should have had strong infection control? Why did the disease seem so contagious in some places, and not at all contagious in others? Did the virus attenuate? Was the epidemiologic behavior due to an unidentified cofactor infection that was common in some places and not in others? (eg. a second virus was needed to develop full fledged SARS).
I can't believe that the infection control measures were so effective. The disease was loose in China for months. Why did it not spread in India at all?A year later I wondered if there were multiple strains circulating, all mutually immunogenic, some more toxic than others. (There may be multiple strains of SARS-CoV-2 as well.) I wondered if that suggested a pandemic management strategy - a kind of "backburning"...
Create a contagious synthetic pathogen that's relatively benign, but induces immunity to the major pathogen -- and spread it actively. I say not entirely novel, because this is how Polio was suppressed. The oral vaccine was an active contagious pathogen that was excreted in stool. It immunized a vast number of persons -- but some became sick, disabled, or dead. When Polio was less of a threat we switched to a non-pathogenic inoculation. The difference is the successful Polio strategy was probably unintentional (I suspect some people understood even in the 1950s), but in the future we'd be deliberately exposing an entire population to an immunogenic pathogen that would almost certainly harm many people.Now we are enjoying COVID-19, the bigger, uglier, brother. Again there's tremendous variability from place to place and time to time. Again India seems unbothered. Again young healthcare workers are vulnerable. Again I wonder if some of the sickest patients have multiple viral inflections or more aggressive strains. Perhaps as our seasonal flu finally fades so will the worst of COVID-19.
I hope this time we'll understand it better.
Sunday, March 01, 2020
India suggests COVID-19 will behave like a bad influenza pandemic
Sunday, February 23, 2020
Someone is hacking at my Vanguard account and Vanguard can't stop them locking me out
Every few days for the past few weeks I have received an email from Vanguard like this:
In other words, not a malevolent hacker, just someone who is not very good with credential management (maybe a bit further ahead on the dementia curve than I am). Based on my username it's probably a distant relative (it's a County Leitrim Ireland name, small cohort). Vanguard should be using time delay management of password attacks, instead they're locking me out. The re-register option is a real nuisance.Our Fraud Team has reviewed your profile and the incidents you described.They have determined that your account was locked multiple times by another client with a similar user name. Fraud has recommend you re-register for account access to change your user name to avoid this situation going forward.
For now I've configured Vanguard to only allow access from my Mac (presumably a cookie). Maybe after a few weeks of getting a different error message my confused relative will figure out they're using the wrong damned username. Then I can try returning to standard access.
Update 3/13/2020: Locked out again, so the restricted access trick didn't help. I'll undo that. I really hate to have to change my username just because Vanguard can't implement 10 yo security technology.
Update 3/28/2020: Finally logged back in again doing the usual reset. Except now I discover the "restrict logon" is implemented by a cookie -- and I cleared my Safari cookies a week or two ago. So even with the reset I can't log in. It didn't work to stop my nemesis, but it sure stopped me.
I had a chance to review Vanguard's troubleshooting pages and looks like they haven't been updated for 5-10 years. So now I have to phone them some time during their limited service hours.
Monday, February 17, 2020
Apple can beat Google Maps -- by investing in bike route maps
But Google has weaknesses. Google maps are increasingly hard to read, particularly in sunlight. Google has no options for scenic routes; even when I choose an alternate route for the pleasure of the trip Google aggressively reroutes me to the fastest option. Apple maps at least have a "no highway" trip option.
These are small weaknesses though. Apple still gets big things wrong even with their latest revisions. Apple hasn't learned much from Google's Local Guides program. My Local Guide score lets me relocate a business in seconds -- something that's made me quite popular with CrossFit gyms and medical clinics that have moved (sometimes they've suffered wrong location listings for months).
Most of all Google has bicycle routes and Apple doesn't. That gap means I can't consider Apple Maps for everyday use. Bike routes are a map moat and Apple hasn't tried to cross it.
But ... Google's bike map moat is silting over. They aren't updating them any more. Google once accepted bike route suggestions from Local Guides -- but now they direct us to treat omissions as road errors and even those are ignored. For example, here's Google's current map of bicycle trails around Hastings Minnesota:
That map makes it seem there's no route from the urban core to Hastings. In fact there's a lovely trail from Hastings to the blue dot on the left, then a brief gravel road, then a trail to St Paul and thus Minneapolis.
Google's neglect is Apple's opportunity. This is an area where Apple could actually beat Google Maps. I think they'd like that.
And, of course, if Apple did make a move maybe Google would accept some improvements ...
Wednesday, December 25, 2019
Bodies are weird, episode 26
My right wrist hurt the other day. A sudden sharp annoying pain. Maybe a tendon, maybe my arthritis acting up.
So I did my usual amateur self-therapy. I avoided the sharp ouch, but I moved with weights and resistance through a proximal path that was sometimes achy but not ouchy. I had lots of opportunities to load the wrist with weights, I am obliged to do CrossFit six times a week [3].
After about 4 or 5 days of this I noticed the wrist was pretty good. No more sharp pains.
It seemed … familiar. Eventually I remembered it happened before, back in Oct 2015, a bit before my formal Dec 2015 arthritis diagnosis. Resistance work was the fix then too.
This isn’t what we were taught in the medieval medical school of my youth. We were taught to rest sore joints, not to put them under painless load. We weren’t taught that running might make knee cartilage better.
Bodies are weird. Back in 2015 my knees were quite sore. I figured my CrossFit days were numbered; I even tried underwater hockey.
But then the knees got better. I continued my back squats and lunges and all the CrossFit rest. Maybe it was the exercise, maybe it was the hydroxychloroquine my atypical rheumatologist prescribed [2] maybe it was both.
Over the next four years I sometimes had knee and wrist effusions, sometimes not. Lots of things came and went. My hands got beat up, but they didn't bother me much.
Then this past summer came around. I felt weaker. My back was fragile in late July. I developed “pseudo-claudication” (look it up). I lost a bet with my daughter when I missed my birthday Bar Muscle Up. I figured age had caught up.
But then it turned out I had the pseudo-claudication was pseudo-pseudo. Probably a protruding disc. It got 80% better after 6-8 weeks of modified exercise and 100% better after 8-10 weeks. (Discs do that — it’s even in the textbooks.) I hit new lifetime best lifts in clean & jerk and back and front squat. Equaled some others. Got even closer to that elusive bar muscle up.
It’s not like I’ve stopped aging. I look a few years older than my age. I feel pretty old. Everything could fall apart tomorrow. So I’m not expecting to carry on like this. I’m just saying bodies are weird and “osteoarthritis” / “idiopathic arthropathy” [2] is weird. We do not understand. We might as well keep moving.
- fn -
[1] The process likely began with some rogue antibodies before 2010 and a single acutely inflamed distal finger joint in 2012.
[2] The one study I’ve seen on HCQ and OA says it doesn’t work. OTOH, I think “osteoarthritis” should be renamed “idiopathic osteopathy” to underscore our ignorance of what’s likely many different conditions with similar appearances. My mother did relatively well on it FWIW — before she went full RA.
[3] I leave it as an exercise for the reader to imagine why a sane person would actually need to go 6 times a week, even foregoing my ice hockey. It’s not for (my) health or training!
Friday, December 06, 2019
The killer application for Apple's AR glasses will be driving
Sucks to get old. At 60 my night vision is probably half of what it was at 25. I drive slowly at night to reduce the risk of missing a pedestrian.
What I need are AR glasses that receive input from forward facing light sensitive sensors and that enhance what I see as I drive. Draw circles around pedestrians. Turn night into day. With the usual corrective lenses of course.
I’d pay a few thousand for something like that.
Seems quite doable.
Monday, September 23, 2019
Carbon sequestration
It’s the year 2,500. Civilization has long recovered from the chaos years following the Trump regime.
Alas, even that catastrophe only transiently slowed CO2 accumulation. It continued for decades near the 2020 height of approximately 4*10^13 kg (40 gT) of CO2 a year.
Happily in 2,500 post-AI solar powered nanotech can extract atmospheric carbon and produce diamond sheets and glues. It’s possible to build a diamond wall to hold back the Atlantic and restore the lost cities of Manhattan and Miami.
How much CO2 would that take out of the atmosphere?
Diamond has a density of 3.5 gm/m or 3,500 kg/m3. If the wall is 1000km long by 50m high by 10m wide it will consume about 1.75*10^12 kg of carbon.
So we only have to build 22 such walls to undo a single year of CO2 emissions.
Update 9/24/2019
I put the numbers into a Google Sheet. Since the wall only required a few weeks of carbon output I decided to try the diamond base of a floating city modeled as a disc with a radius of 50km and a depth of 200m. That did the job!
A single floating city absorbed 145 years of 2018 carbon production.
It would be easier, of course, to build something attached to a landmass, but where’s the romance in that?
Friday, September 13, 2019
Clark Goble 1967-2019
Clark and I had different opinions on the future of ISIS. This was years ago, when we conversed often on app.net/ADN. He under his own name, me, less boldly, using my John Gordon pseudonym. (Clark knew I was John Faughnan, we corresponded by email too.)
Clark was a slippery fellow in a debate so I suggested a wager based on the state of ISIS in a year or so. I forget what I wagered, but Clark offered to pay off in Amano artisan chocolate. His company’s chocolate that is.
Some time later, a bit prematurely I thought, Clark decided I was right and he shipped me a wonderful supply of some of the finest chocolate I’ve ever had. I tried to stretch out the supply but I’m bad with chocolate. I ate it too quickly.
I was in Clark’s debt after that. I thought I’d have a way to pay it back, but I didn’t expect that to be a donation to his posthumous gofundme account. He died 9/6/2019 of a ruptured cerebral aneurysm. He was 52yo, married, with five children.
My wife’s mother died the same way at the same age. I remember, from medical school days, a young woman dying suddenly the same way. It’s like being hit by lightning. Here one day, gone the next.
I never met Clark in person. We chatted for years on app.net, then continued on Twitter. We had some things in common. We both loved the outdoors - mountain biking and, in his case, mountaineering. We enjoyed science and especially physics — though he was the real thing and I am just a hobbyist. Both of us were happy fathers; Clark's youngest child was about a year old when he died.
We were both born in Canada. We both liked travel, he wrote often of his mission work in Louisiana.
Politically and spiritually we were pretty different. Clark took his faith and Mormon theology seriously, I’m a functional atheist. Clark was a Western old school Republican, I’m an Obama-Democrat. Many of our discussions were on politics — he loved the ins and outs of democracy.
I miss Clark's voice. I’m sad I’ll never get to drop in for chocolate. I mourn for his family and all who loved him.
Monday, September 09, 2019
Bicycling North Dakota's Maah Daah Hey trail with Western Spirit
Last week I bicycled most of North Dakota’s Maah Daah Hey trail. The New York Times’ John O'Connor described it in 2018 (emphases mine) ...
… One moment I was bouncing along, knee-deep in sagebrush, mind reeling from all the natural beauty zipping by, and the next I’d caught a wheel on a rock and gone sailing into that familiar somersault: butt rising from the saddle, shoulders twisting violently, hips lurching up-and-over, heels actually clicking midair, sunglasses and water bottle and half-eaten Clif Bar hurtling into the trees, the ground closing in...
… it had been my idea to cycle the Maah Daah Hey Trail, the longest and arguably most grueling single-track mountain biking route in the United States...
… I was an unlikely candidate for the trip: I had never ridden a mountain bike before, or even camped much….
I read that introduction before the ride and I scoffed. How would O'Connor know about going OTB (over the bars) if he’d never ridden a mountain bike? And wasn’t riding a “grueling" single-track absurd for someone with no prior experience?
So of course I went OTB on my first day on the trail. Damn water break bumps, I really didn’t know how to ride them at speed. I learned.
Anyway, after doing that trail outfitter glamping style I gotta admit that while O'Connor doesn’t have the best judgment, he is pretty tough.
I could write a lot about the experience. The crew I rode with were each worth a story of their own! Alas, I don’t have the time or talent to do that justice. Instead, since I’ll share some things I wish I’d know before the trip.
There are two full service outfitters that supply guides, food and water, and gear transportation. I used Western Spirit, but I’m told the competition is also excellent. Dakota Cyclery will do gear transportation but no longer does guiding, I think it works with both outfitters.
This was my first experience with an adventure cycling outfitter. Some things I didn’t know:
- Our guides were superb. They were also extreme athletes, so they have different attitudes towards “steep” and “exposure” then civilians.
- The foot is amazing — quality, quantity, variety. Our guides really knew how to cook. Probably 4000-5000 calories a day plus gel packs, snacks, bars, etc. I neither gained nor lost weight and I ate a lot.
- I drank 4-5 Liters on a hot day and I was still behind. Have a big hydration pack and make sure you fill it. The guides expect you to know to do that.
- Guides supply gel packs and sunscreen, but to be safe you should carry your own as well.
- Bring your own derailleur hanger. They don’t have those for every bike. Also a replacement chain link in case the join link brakes.
- You are expected to tip. I’m not sure how much, but on a $1200 tour 15% is about $200. The ideal is one rider collects funds and presents them as a single gift. Have cash with you.
- One guide rides sweep and one rides truck. Unless you’re dead last you may be well ahead of the guide. Some days I had a lot of time alone on the trail.
- You can bring a four person / family tent, it doesn’t have to be a backpacking tent.
- We didn’t do the whole trail. We started at a camp site about 16 miles south of the Northern CCC terminus, so south of China Wall (never saw it). They did a Friday ride on a different but really excellent trail that was basically a sub for that segment.
- My companions were older than I’d expected and they were all more skillful than me. Of our group of 7 four were over 60 including our best descender. I think mountain bikers do the Maah Daah Hey when they’ve done everything else many times and are looking for something different.
Maah Daah Hey notes
- The trail doesn’t seem technical compared to Sedona or Moab, but it has its own challenges. There are a lot of steep climbs with marginal traction — only the super-strong and skilled can nail every one. There is exposure on loose surface tight off-camber downhill hairpin turns. There are deep ruts that suddenly appear along the trail that you don’t want to hit at speed. The working trail itself is effectively narrow, a tire worn 8” dirt path with grass alongside. You need a smooth pedal stroke and good control to avoid hitting the grass ledge along the trail.
- Unless you’re really good you can’t look around and ride, you need to stop to take in the scenery.
- Everyone in my group had a modern XC/Trail bike — dropper post, 1x12, tubeless, full suspension, 29” wheels, slack geometry. Everyone … except me. My bike was out of the mists of time. If you don’t have "that bike" I recommend renting from your outfitter or Dakota Cyclery.
- Flats or Clips? Most do Clips, I did Flats because I was willing to sacrifice some climbing power for faster exits. Clips make for smoother pedaling though, and make it easier to stay on the narrow trails.
- If it rains you are screwed. The trail has been getting more rain the past few years … which makes the landscape surprisingly green but the trail unrideable. The Bentonite soil turns to cement, only a very strong rider with lots of frame clearance can get anywhere. Rain is the achilles heel of the Maah Daah Hey. We were lucky to have only one rainy day and 2-3 h of hike-a-bike. If rain persists outfitters bail to hikes and gravel rides. It’s a risk.
- In September there were almost no bugs at our campsites!
- You don’t see bison. This is ranch land, bison are not welcome. You see lots of very healthy and powerful looking cows and maybe some gazelle. We heard lots of coyotes but didn’t see any.
- We met 2-3 people total on the MDH trail over 4 days. There were hunters at the campsites; they campsites are all reachable by road.
- We crossed the Little Missouri twice carrying our bikes, there are multiple stream crossings. Don’t try to ride across, you’ll get mud everywhere.
- You can get lost. The trail is well marked until it isn’t. It’s good to have guides. There are one or two spots that could kill someone moving fast in the wrong direction.
- The landscape is more diverse than I’d expected. Badlands, grasslands, even some thin forest. It really is beautiful to ride across, not least through the wide grasslands.
- I bought inexpensive sun sleeves and a weird geeky neck/ear sun cover that fit under my bike helmet. They were great.
More updates and revisions to some … if time allows ...
Saturday, August 17, 2019
Sorrow for the Long Tail - the memory machine I will never see
There are several software products I want nobody will build.
For example, I want a “screen saver” that will randomly select from a collection of video and still images and display them across multiple screens.
Pretty much like Apple’s annoying [1] screen saver, but for video it would randomly select a xx second file segment and play that without sound.
I don’t think anyone will ever build this. It’s too hard to do [2] and there’s no money in it. Only a small number of people would pay, say, $20 for this. Maybe 1 in a 1000. After expenses and marketing it would be hard to earn even a few thousand dollars.
Which reminds us of the false promise of The Long Tail. Those were the days that Netflix had a huge catalogue of barely viewed movies [3] that were often very fine. We thought there would be business for the interests of the 0.1%. That didn’t happen.
This is why I’ve given up on trying to predict the future ...
--
[1] Whenever macOS cannot connect to the folder hosted on my NAS it reverts to the default collection. I need to restore my share and I’ve never been able to find an automated way to do that. On iOS things are much worse. Speaking of products I want, I’d pay $20 for a macOS utility that that simply reset my screen saver to my preferred share.
[2] We never thought software development would keep getting harder. We used to think there would be a set of composable tools we could all use (OpenDoc, AppleScript, etc). We expected a much more advanced version of what we had on DOS or Unix in the 80s or the early 90s web. Instead we got AngularJS.
[3] In the mailer days our kids movies were unplayable due to disc damage about half the time. Finally gave up on that.
Monday, August 12, 2019
Rough personal notes on review of management of degenerative lumbar spondylolisthesis with lumbar spinal stenosis and pseudoclaudiation
Every so often I review a medical topic and stick my notes into Simplenote for later reference. The reviews are quite messy since it’s just for my use. For what it’s worth, some hasty notes on this topic.
IMAGING
Initial Plain film: spondylolysis/listhesis. Standing flexion/extension lateral plain film, oblique (for pars interarticularis), AP for severity. (or just lateral, oblique and AP). See https://emedicine.medscape.com/article/2179163-workup
Considering surgery: MRI (neurosurgeon will have preferences)
---------------
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270383/
Degenerative spondylolisthesis - European perspective - 2008
“Symptoms of neurogenic claudication that cause the patient to stop and sit after less than two blocks of walking usually correspond to the time, when the patient consents to surgery …
…. The plain radiographic features include the essential finding on a lateral view of forward displacement of L4 on L5 or, more rarely, L5 on S1 or L3 on L4 in the presence of an intact neural arch. Defect of pars interarticularis (which has the appearance of a Scottie dog with a collar) that can be seen on lateral or bilateral oblique views helps to distinguish between DS and isthmic spondylolisthesis …
… Only 10–15% of patients seeking treatment eventually will have surgery…
… The intervertebral spaces of the slipped segments were decreased significantly in size during follow-up examination in patients in whom no progression was found. LBP improved following a decrease in the total intervertebral space size. The development of osteoarthritic spurs, hypertrophy and ossification of the intervertebral ligaments, and facet arthrosis may lead to secondary stabilization that prevents slip progression…
Indications for surgery:
1. Persistent or recurrent back and/or leg pain or neurogenic claudication, with significant reduction of quality of life, despite a reasonable trial of non-operative treatment (a minimum of 3 months).
2. Progressive neurological deficit.
3. Bladder or bowel symptoms.
--------------
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357993/ (2019 review, neurosurgery)
A systematic review of the literature has shown that delaying surgery for a period of conservative management is not associated with a worse surgical outcome and that surgery is more effective than continued conservative treatment when conservative options have failed for a period of three to six months…
… minimally invasive surgical approaches that preserve stabilizing paraspinal musculature …
————————
Some other odds and ends:
- We suggest that the angular instability of the intervertebral disc may play a more important role than neurological compression in the pathogenesis of disability in degenerative lumbar spondylolisthesis (this was weird — from MRI study of axial loading)
- Vanderbilt neurosurgery study from 2014 claimed medical management didn’t work but it looked like a horrible study
- BMJ review of 2016 was down on non-surgical treatment but not super keen on surgical. Consistent with trying conservative management for some time before trying surgery.