Saturday, July 27, 2013

My eBook misadventures. Not ready yet?

After much thought, I decided to build my digital library on DRM-free EPUBs. That means buying from DRM-free sources like TidBITS, O'Reilly, and some science fiction books from Tor/Forge or buying from Adobe Adept DRMd Google Books and using DeDRM.

It was a relief to get that all sorted out. Now I just needed a handheld eBook Reader other than my too small iPhone 5 [2]. I gave up on the Nexus 7 last year, and I don't love the current crop of iPads [1], so I took the advice of some appnetizens and tried "freedom-friendly" Kobo. I really like the idea of moving EPUBs on and off the device with a simple SD card.

Alas, Kobo seems to have abandoned the US market. I found some dusty old Kobos at a local independent bookstore, but one was broken and the other was too small. I tried ordering the HD Aura but Kobo's webstore checkout failed repeatedly. Then I tried to order a Kobo Glo on NewEgg and found they were selling a $120 device for $150.

I finally decided Kobo has effectively exited the US marketplace.

Then I thought the Nook might be the closest thing to an American Kobo - never mind that B&N is at the edge of extinction. I ran off to my local B&N (once we thought these were scary, now, like Microsoft, they seem sad and vulnerable) to give an eInk Nook a try.

The page turn flicker killed me. I felt like someone was tapping my head with each page turn. Maybe there was something wrong with those floor models, the wee Kobo I tried didn't seem so bad.

That leaves the Amazon Paperwhite. I've already sold my soul to Apple, I don't need another closed shot wannabe monopoly owning my stuff.

Which brings me back to those iPads I don't like, or the new "retina" Nexus 7.

Or I could wait anther six months.


[1] The Mini seems small and isn't Retina. The iPad Retina is too heavy. In both cases I really miss the convenience of a simple SD card.

[2] The iPhone 5 has the right screen, but for technical book reading I need something bigger. 

Monday, July 22, 2013

Nose and mouth breathing: a popular non-medical topic and a curious research deficit

For idiosyncratic personal reasons I've had to think about mouth versus nose breathing during wake and sleep. Despite my medical background this is a novel topic for me; but a quick Google search shows there's lots of lay interest in the topic. As I discovered, this interest is not matched by much research.

I remember learning in medical school that infants are obligate nasal breathers, but we assumed adults had options when both awake and asleep. That's not entirely clear, a tiny 9181 suggested  at least some adults are obligate nose breathers during sleep ...
The effect of nasal packing on sleep-disordered... [Laryngoscope. 1981] - PubMed - NCBI 
... Nasal obstruction is known to cause abnormal ventilation during sleep in infants, but its effects on breathing and oxygenation during sleep in adults are unknown. However, in adults, obstruction of the nose by nasal packing has been shown to cause hypoxia, and on occasion, hypercarbia and sudden death. We have investigated the pattern of ventilation and the level of oxygenation during sleep in seven patients who had nasal packs after nasal polypectomy or septoplasty. ...  Nasal packing either caused or worsened sleep-disordered breathing in all patients and significantly increased the number, duration, and frequency of episodes for the group as a whole. Several patients also had a greatly increased number and severity of episodes of nocturnal oxygen desaturation....
Of course patients selected for polpyectomy are not typical; particularly in 1981 many who received surgery would today be treated as having obstructive sleep apnea. The 1981 study was repeated in 1991 with essentially the same results. Once again these patients had a surprising amount of trouble switching to mouth breathing during sleep. It's almost as though obligate nasal respiration persists in some adults throughout their lifetime.

And that was most of what I could find in my quick look, other than some review articles [1]. They probably have more references, but in the abstracts they mostly call for "additional research". Not much new knowledge in 33 years. I wonder what medical textbooks teach today.

Medical research is strange. My own suspicion is that a significant number of adults are essentially obligate nose breathers during sleep. It would be good to have some data.

- fn -

[1] 30+ years of research ... 3 reviews with limited follow-up.
  • Mechanisms of nasal obstruction in sleep. [Laryngoscope. 1984] - PubMed - NCBI. ... If airflow resistances are increased by nasal disease, complete inspiratory obstructive closure of the pharynx and apnea can result from nasal breathing in sleeping subjects. Recumbency increases resistive swelling of inflamed nasal mucosa. Furthermore in patients with normal mucosa and unilateral nasal obstruction, contralateral recumbency induces contralateral obstruction which increases resistance to nasal breathing; and in either dorsal or lateral recumbency the congestive phase of the spontaneous nasal cycle acts in a similar way. Examples of breathing disorders in sleep and impaired quality of sleep in patients with obstructive mucosal disease and both bilateral and unilateral structural abnormalities are cited.
  • Nasal obstruction as a risk factor fo... [J Allergy Clin Immunol. 1997] - PubMed - NCBI. Similar to above.
  • Sleep, breathing and the nose. [Sleep Med Rev. 2005] - PubMed - NCBI ... In normal subjects, the nasal part of the upper airway contributes only little to the elevation of the total resistance, which is mainly the consequence of pharyngeal narrowing. Yet, swelling of the nasal mucosa due to congestion of the submucosal capacitance vessels may significantly affect nasal airflow. In many healthy subjects an alternating pattern of congestion and decongestion of the nasal passages is observed. Some individuals demonstrate congestion of the ipsilateral half of the nasal cavity when lying down on the side. Nasal diseases, including structural anomalies and various forms of rhinitis, tend to increase nasal resistance, which typically impairs breathing via the nasal route in recumbency and during sleep. A role of nasal obstruction in the pathogenesis of sleep-disordered breathing has been implicated by many authors. While it proves difficult to show a relationship between the degree of nasal obstruction and the number of disturbed breathing events, the presence of nasal obstruction will most likely have an impact on the severity of sleep-disordered breathing. Identification of nasal obstruction is important in the diagnostic work-up of patients suffering from snoring and sleep apnea.
  • a 2012 Outside magazine article is a surprisingly good evidence-based review of mouth/nose respiration during exercise, and whether one could deliberately modify that respiration ... "I have never seen a study—and I look for them—in which any adopted pattern of breathing did anything to performance, oxygen consumption, efficiency, or fatigue."

Some post-publication discoveries, I'm going to see if I can get copies of these ...
Update 7/23/13
I'm back from my rushed and unjust survey of the literature. My working conclusions are unsurprising:
  • The experimental data is very limited, and there's not much evidence any treatment other than CPAP helps many people with "sleep apnea"
  • It's not clear what "sleep apnea" really means, there are probably multiple causes that contribute to a similar clinical presentation. It's not clear that we have the best treatment for every cause.
  • We know that some infants can switch from nose to mouth breathing and we know that some adults have a lot of trouble with nocturnal mouth breathing during acute nasal obstruction. We don't know if they do better over time.
  • Over a 20 year period there's often confusion between sleep disturbance, nocturnal oxygen desaturation (not to mention altitude effects), and apnea. There's also confusion between acute and chronic responses.
  • North American clinicians have mostly lost interest in nasal obstruction syndromes and assume they make no contribution to nocturnal oxygen desaturation or even sleep disturbance. International clinicians still suspect nasal obstruction plays a role in some oxygen desaturation. Nobody seems interested in mere sleep disturbance without desaturation or apnea.
It's pretty much the picture I get when I look at most surgical conditions (someday I should go over my review and management of the ganglion cyst).

Update 7/25/2013

I don't see this in the ENT literature, but given renewed interest in hypertonic saline irrigation for chronic sinusitis, I wonder about use for nasal obstruction and sleep disturbance ...

Tuesday, July 09, 2013

Bicycling in a deluge

Many years ago I road through a mini-flood downpour. Not the nearly 5" that drowned Toronto, but a fun storm. That was it for a long time. In our old midwestern climate a genuine deluge was really not that common. They were easy to dodge, and with fenders and some gear routine rainfall is no problem.

Things are different now. In the post-400 ppm CO2 world my weather is warmer and wetter; we are told to expect really heavy downpours more often. Like the one I hit last week on my routine commute. Instead of waiting for it to pass I rode on, and so I  found out what gear worked and what gear didn't.

Didn't work
  • Old baggies: They degrade with age. The ones I had in my front bag were worthless
  • My brakes and my vision: Of course both brakes and vision degrade in rain, but in a deluge they really do nothing. This was a bit of a problem because in 3" of a groundwater collection my tires didn't have much traction, and I couldn't see a big pothole under the floodwater. So I went down.
  • My GoreTex shoe covers: They didn't work because I didn't put them on. That was dumb -- my shoes didn't dry off for a couple of days. Even though the rain was mostly fun, it would have been nice to have dry shoes for my return trip.
  • My panniers: They do well in routine rainfall, but I knew they weren't waterproof. I poured a half-inch of water out of my front bag. My wallet, keys (no electronic fob!) and several maps were soaked; I tossed the maps.


  • My waterproof iPhone 5 case: Best $15 I've ever spent. If not for that case my phone would have been ruined. I leave it in my bike bag.
  • A rubber lined "conference bag" that I was carrying my work laptop in the rear panniers. This was dumb luck, I had no idea that bag was so water resistant. If I'd been thinking I'd have waited out the heavy rain rather than chance losing the laptop.
  • Fenders: No wheel tracks, though in that amount of rain I suppose they'd have washed off.
  • My yellow rain jacket and lights; Not sure the lights were visible, but I think the jacket was. In any case I opted for the sidewalk when the road narrowed, figured drivers couldn't see at all. I wasn't that worried about staying dry, but the ancient Nashbar jacked did that too.
  • Helmet and helmet cover: I bonked the helmet when I went down, which made me feel better about having it. Helmet cover worked better than I'd expected.
  • Synthetic clothes: Wow, that stuff dries well.
Falling was a drag, but I wasn't hurt and now I know what to look for - road floods are trouble. I should have moved to the nearby sidewalk. I had to relube my bike, but that's not a big deal (yay sealed bearings) - so, overall, it was kind of fun. Next time I'll have a canoe bag in my rear pannier -- something to hold wallet, keys, garage door opener, maps and similar items during a real downpour.

Saturday, July 06, 2013

National Library of Medicine adds PubReader - Instapaper for medical literature fans

I became a fan of the National Library of Medicine (NLM) when "Grateful Med" [2] augmented the old telnet interface to what was then MEDLARS/MEDLINE, and once was Index Medicus. Rose Marie Woodsmall recruited me to teach rural docs how to use Grateful Med --  which was kind of excruciating in the days before error correcting modems [1].

I loved it when the NLM added RSS feeds to PubMed results, so I could track research topics in my feed reader (still works in Feedbin/Reeder). That's where most of my | [3] medical posts come from.

Most recently, in the post-2007 age of full text access, NLM has added an HTML5/CSS3 Instapaper-like view for reading articles on mobile or desktop. It's known as PubReader™ (emphases mine):

... view is available for any article that is available in full-text HTML form in PMC. It is not available for older content that is available only in PDF form or as scanned images of the original print pages. You can get to the PubReader view directly from an article citation in a search result list or an issue table of contents:

Or from the Formats links in the top right corner of an article page in PMC...

...  PMC now automatically directs certain users to the PubReader view:

- everyone using PMC on a tablet or mobile device, and
- a small, randomly selected sample of people using PMC on a desktop or laptop....

.. We start with the XML version of an article and use XSLT to convert it into an HTML document. We then add CSS and Javascript (JS) to implement the formatting, paging, navigation, text reflowing and other dynamic features. This, essentially, is the way we have created the traditional article display in PMC for years. The difference now is that we are able to take advantage of features and functions that are available only in the latest versions of the underlying technologies (HTML5 and CSS3).

The CSS and JS code used to create a PubReader presentation is available at the GitHub repository NCBITools/PubReader. Anyone can use or adapt it to display journal articles or other content that is structured as an HTML5 document.

Great service, neat technology.


- fn -

[1] In response I reinvented software error correction in the early 80s. That seems stupid now as the work had been done decades before, but it's hard to remember what life was like before we could discover knowledge in seconds -- assuming we know the magic words.  We really don't understand, yet, how much that has changed our world.

[2] Rose Marie was a deadhead (probably still is), which was how the DOS, later MacOS, app got its name. In 1996 Internet Grateful Med, an early web app, displaced it. In the 00s we got today's PubMed.

[3] All of which have, I'm happy to say, RSS feeds -- even which started out without. is probably the best to follow with a feed reader.

See also:

Friday, July 05, 2013

Acute back strain management - one anecdote

After the 2008 vacation ambulance ride and the supine drive home I decided I needed to see a doctor other than myself. Twenty-five years of increasingly severe and transiently disabling back pain was enough. So I did, and I got better.
Which nobody wants to hear about. There's nothing more boring than back pain stories. Heck, when I first saw my back doc he cut me off at the start of my epic. He'd heard it all before. 
So nobody wants to hear my stories, but, honestly, if you have back pain you should read 'em [1]. I got anecdote, I got training, I got experience, and my current approach is consistent with PNBC's evidence-based back strength boot camp. By contrast much physician management of acute back strain is pretty weak.
This particular story is a bit different. In the past I'd sneeze or tie my shoes funny and be laid out for days. [2]. This time I was at the end of four sets of CrossFit front squats, lifting about 125 lbs. when I shifted forward a bit, tried to correct and felt my back tear (or whatever it's doing - we don't know). I dropped the bar and lay (grammar?) down on an ice pack. 
This is what I did for immediate post-injury recovery. This time I didn't need my old canes, and two doses of Motrin was plenty. I don't know if that's because I'm stronger than I once was or because this was a relatively minor injury.
  • Sunday (injury day): neoprene waist band and doubled cold pack. Walking and modified version of my usual morning stretch [4]. Inline skating in pm - that's often helpful for me [5]. Sleeping was difficult, though I've had much worse. Motrin 800mg midnight.
  • Monday: I am able to stand. Fear level diminishes.  Able to do most of stretch [4]. Continued ice. Evening skate with my son and the Minnesota Inline Skate Club. Start using Roman Chair for extension exercises, with arm assist. Motrin 600mg before bed.
  • Tuesday: I am able to do 85% of my usual stretch. Minimal ice. Two hour high speed bike ride from home to Minnehaha trail to Lake Harriet around and back. Roman Chair with minimal arm assist. No meds, sleep a bit sore.
  • Wednesday:  AM full stretch routine. 16yo and I go to weight room at JCC. There I can do arm workout, resisted back extension, abdominals with controlled equipment (not free weight). Full Roman Chair. In evening I'd scheduled a swim, but couldn't fit it in. PM stretch. Sleep good.
  • Thursday: AM stretch, otherwise day spent on chores and family duties. Full set of situps and Roman Chair. PM stretch.
  • Friday: AM stretch, AM CrossFit Yoga - extreme stretches. No pain. Two hour bike ride in evening with 16yo. Roman Chair and Situps. PM stretch. Back isn't normal, but it's pretty good.
  • Saturday (plan): Try running to barber shop in AM. PM family bike ride -- lots of lifting bikes, moving car seats. Good functional back test. 
  • Sunday (plan): Regular CrossFit -- will keep weights under 50 pounds (women's 18 or 33 lb bar).
As a rule a soft tissue injury at my age will take at least six weeks to heal. In addition it's clear that my back is going to need to get stronger before I go back over 100 lbs [6]. So my go forward recovery plan is:
  • Maximal weight 90lbs until my extension and abdominals are much stronger.
  • Ensure I have at least 3 days between my full CrossFit workouts. They are intense and I need that much time to recover; when I was hurt I had a 1 day gap. In between I do my bike rides, inline skating, and, now, gym weights.
  • More aggressive Roman Chair and situp training.
  • Add 1 day/week of workout in conventional gym with controlled equipment. I will establish my current baseline max for 6 rep extension and abdominal. I need to increase that by 30% before I go up again on free weight.
  • Consider adding a routine CrossFit Yoga session -- if I can find the time I think that would be a good complement in a couple of ways.
- fn -
[1] For example ...

[2] One of the little ironies of mortal life is that nature routinely does stuff to us that, when we do it to one another, could be considered a war crime.

[3] Why is CrossFit, and why am I doing this when I'm older than the moon? I've got a post pending on that.

[4] Every morning, 5 reps each for past five years: Knee to chest r/l, knee lateral hip rotation r/l, straight leg, two leg to chest, elbow press back extension, full arm back extension, cat stretch, sit rotate, hamstring stretch, quad stretch.

[5] Sounds bizarre, but when I've hurt my back it's a lot easier for me to skate than to walk. I'm a good skater. It also forces me past the fear that accompanies this kind of injury, especially for those of us with memories.

[6] My classes are about half female, and, prior to my injury, I lifted an average or above average amount for the female group. Bottom of the male group of course.

Update 3/19/2016

Despite developing an inflammatory osteoarthritis (yay) my back has done quite well over the past 3 years of CrossFit. I had another strain with deadlift in Jan of 2016 but it healed well. I think I took 1-2 weeks off CrossFit to do cyber-type weights at a different gym before returning to CrossFit. Year 8 post my great PNBC experience and 3 years of CrossFit St Paul my back is healthier than most people my age. 


Tuesday, July 02, 2013

American psychology and civil war in Egypt

An acquaintance from my Quebec High School is active in Egypt's secular resistance to Morsi's rule. She's frustrated by Obama's tolerance of the Muslim brotherhood; I think she would prefer the freedom rhetoric of Bush II. Personally, I prefer Obama.

That's not what's interesting though. The interesting bit is she seems genuinely confident that Egypt won't break down, like Syria and Iraq, into civil war. That confidence seems strange to an American, even an immigrant American like me. We believe in Civil War; we had a big one not long ago. There are still flare ups in old battlefields.

For an American it's easy to imagine Civil War in Egypt. There are many things that are strange to us, but not civil war.