Sunday, August 11, 2013

Judo techniques - Free to use illustrations

Previously on Nephrophysiologist we looked at some free judo illustrations that our club were potentially going to use for grading hand-outs. The number of illustrations has grown steadily, but the first actual use the pictures have seen is the poster at the top. It isn't half-bad if you ask me, but then I may be biased.

Work-wise the bulk of the time was spent trying to re-size all pictures so that the figures appear to be about the same size. Then a quick levels adjustment to get rid of the slight gradient that Art Rage uses for a background, and a hue/saturation adjustment to make the blue gis blue rather than purple. Finally I had to trace-down the font used for an old club T-shirt. After much searching and many, many pages of fonts a friend of a friend identified it as Grenoble. Then it was easily found at our friendly font repository.
To finish off I would just like to remind everyone that there is a repository of free, as in speech and beer, judo illustrations to be had under the Creative Commons - attribution, share-alike - license on and most of them can also be found at the wikimedia commons. This here below is sasae-tsuri-komi-ashi perhaps done best in the history of the world by Muneta Yasuyuki. However, it usually looks more like slow collaborative falling.

Monday, August 05, 2013

Books for anaesthesiology - General textbooks

Having properly started my residency in anaesthesiology and intensive care medicine I have started looking for textbooks to help me.

In my view medicine has four important levels of knowledge: basic science, clinical practice, evidence based medicine, and epidemiology. Clinical practice will be the focus of your general textbook, but each level deserves its own book because the general textbooks are never good enough. For basic science and EBM the demand for detail and precision is much greater, and epidemiology is often ignored completely.

What follows will be a number of book-reviews of books that I have read, which are useful for anaesthesiology residents. If you have any suggestions, please leave a comment.

So far I have these three general anaesthesia books, which I will say something about.

Morgan & Mikhail's Clinical Anesthesiology (2013, 5 ed. edited by John F. Butterworth IV, David C. Mackey and John D. Wasnick), which is actually available in electronic form through the university library. It's an easy read, unless you are easily annoyed by typos and trivial errors. Instead of references it has suggested reading, which is a mix of reviews, book-chapters and original research. To say that it lacks depth is to state the obvious, but it seems to reflect the state of clinical anaesthesia fairly well.

With that I mean that there is sufficiently scarce evidence that the personal opinion and experience of the individual mentor makes huge differences in how and what you are taught. It is a bit annoying, because you spend a couple of weeks with one specialist behind you, until they are confident to let you run things. Then you change to the next specialist, and they basically think you are insane.

Anestesi (2005, 2 ed. edited by Matts Halldin and Sten Lindahl), a swedish textbook, which is helpful for some practices that are more specifically swedish, and it is generally a good book. Not very thick though, so rather basic.

Anestesikompendium (2004, 8 ed. edited by Rainer Dörenberg), the pocket reference produced by the department in Uppsala. It's brilliant for working in Uppsala for obvious reasons, and includes important practical knowledge like which syringes to use for which drugs, and pre- and postoperative guidelines for different operations and different post-op wards at the hospital.

This early in the residency I am in a read and re-read mode for trying to remember and understand the different anaesthetic regimens and why different specialists prefer different ways of doing things, so it is a good thing to have a couple of books to compare. However, in many cases where practice is significantly different between different specialists they give no, or little guidance, which is why I am seriously considering getting a more complete work. Like 500 pages thicker Clinical Anesthesia by Barash and coauthors, or the two-volume over three thousand pages thick Miller's Anesthesia. In addition there are more specific books covering specific subfields of which I will write more later when I have had time to read them.

Sunday, July 28, 2013

Are the exercise recommendations insane?

I try to stay fit. I lift weights. I do crossfit. I do judo, and I still practice at a fairly respectable level. Since I found the training diary Funbeat about two years ago I have been keeping a detailed training diary. Recently I went through my training statistics and came up with some interesting numbers. In the last two years I have trained 262 times for a total of 285h 29min. That comes out to about 23 minutes per day or 164min per week on average.

Now, let us have a look at the exercise recommendations from the World Health Organization, Centers for Disease Control, or the Swedish equivalent Folkhälsoinstitutet. Here follows the text from the WHO, the others are exactly the same.

Adults aged 18–64 should do at least 150 minutes of moderate-intensity aerobic physical activity throughout the week or do at least 75 minutes of vigorous-intensity aerobic physical activity throughout the week or an equivalent combination of moderate- and vigorous-intensity activity. Aerobic activity should be performed in bouts of at least 10 minutes duration. 
For additional health benefits, adults should increase their moderate-intensity aerobic physical activity to 300 minutes per week, or engage in 150 minutes of vigorous-intensity aerobic physical activity per week, or an equivalent combination of moderate- and vigorous-intensity activity. 
Muscle-strengthening activities should be done involving major muscle groups on 2 or more days a week.
We immediately notice that I follow the minimum guidelines of 75 minutes of vigorous-intensity aerobic activity, and two days with muscle-strengthening activities. But we cannot say that I fulfil the guidelines for additional health benefits. On average I do 164 minutes of exercise including strengthening activities. Of course, we might argue that I ride my bike to work, walk the dog, and go shopping so that I easily fulfil the quota. However, the guidelines specify at least ten minutes duration, and in the complete text specify that you should raise your heart rate and break a sweat. Even going as far as specifying that just shopping or walking the dog does not count for most people because the intensity is too low, so that argument does not work.

In the end we must find that I have a hard time keeping up with the guidelines. At the same time, with that activity level I am able to practice judo with our ten to twenty year younger elite and junior players. I am stronger than I ever was, and have as high endurance as I have had since I stopped swimming. For those (like me) who like numbers that means a 170kg dead-lift, a 90kg bench-press and a 124kg back-squat, and endurance-wise a VO2max of around 60ml/(min*kg). Nothing spectacular, but clearly very fit for a 35-year-old nephrophysiologist.

How can we possibly expect our patients, and the public in general to be able to train that much? And, would I actually increase my expected life-span and number of healthy days by more than doubling my training? For breast and colon cancer the guidelines say:

Data indicate that moderate- to vigorous-intensity physical activity performed at least 30–60 minutes per day is needed to see significantly lower risks of these cancers.
60 minutes per day? On average? For enough time to affect cancer mortality? Who the fuck even completed these studies?

Friday, July 26, 2013

Newton's law of cooking chicken

Newton's law of cooling can be used to predict the time of death from the temperature of a corpse and the ambient, which is a silly and boring example. On the other hand, when we are cooking chicken and our better half asks when it will be done (and demands that it be done in a given time), then it becomes an interesting and useful equation. Let us say that it has already cooked for almost an hour, it is around half past seven, and dinner is supposed to be at eight.

The important point is that Newton's law of cooling is equally applicable to cooking because physical law is symmetrical, which means that cooling and heating behaves the same way. The law states that the rate of change of the temperature of an object is proportional to the difference between its own temperature and the ambient, or
dT(t)/dt = -k(T(t)-Tambient)
where T is the temperature of the object, t is time, k is a constant, and Tambient is the ambient temperature. It is a differential equation that solves to 
T(t) = Tambient + (T(0) - Tambient)e-kt
which we can use to calculate the temperature we have to cook the chicken at to be able to serve dinner at eight(-ish). The only problem is that we have to know the constant k which is specific to the particular chicken and filling we have in the oven. Luckily, we used an oven-thermometer, and we kind of remember how long it has cooked already. So, if it took 50 minutes to go from 10°C to 53°C with the oven at 150°C then we can calculate the constant as
k = -1/t ln((T(t)-Tambient) / (T(0)-Tambient))
that is
k = -1/50 * ln((53-150)/(10-150)) = 0.0073 min-1
In turn, we can use this to calculate what temperature we have to use for the chicken to be done in another 30 minutes as
Tambient = (T(t) - T(0)e-kt) / (1 - e-kt
 which gives
Tambient = (80 - 53*e-0.0073*30) / (1 - e-0.0073*30) = 200°C
Luckily, we didn't have to do the calculations by hand because a bigger nerd than us have created a web-app where we just plug in the known values and get the missing one for free.

Finally, here is the money-shot.
Science, because it works bitch.

(Although the higher temperature did burn the skin a little bit, and it would have been jucier if it had cooked at 150°C the whole time.)

Wednesday, July 17, 2013

A matter of questionable importance

One of the most important aspects of reading is to have a good place to read. Crazy, you say. Any place is a good place to read, and of course you are right. When I was younger I would read all the time and everywhere, walking around bumping into people, missing my bus-stops, and getting reprimanded in class. Indeed every place was a good place to read, but now it's different. Wherever I find myself I have somewhere else I should be, or I have something that more or less urgently needs to get done. So when at home, when at rest, a special place to sit and read and think is an important thing. A place of solace (A fortress of solitude! No, too much?).

It is obviously not as important as roof over your head or food and clean water, but important never the less. For years I haven't had one, and I haven't read as much as I used to. It has simply not been a priority when furnishing the flat.

Anyway, we were at IKEA the other day and there was this new armchair model. Simple, not overly large, really cheap, and above all with side head-rests. I had to have it. There have been a number of armchairs I have had to have over the years, but since this was simple, small and cheap I could buy it on impulse. Now I have the ideal reading corner, and it complements my life-sized decorative boxer perfectly. It is close to my books, but not the work books, and it is far away from the computer and the heaps of manuscripts, applications and statistical analyses to be worked on.

I do have a small confession to make. I am writing this in said chair, and I did just check my mail, but then rules are made to be broken. Especially small silly rules with no real fundamental importance. Anyway, there shan't be too much work done here, and I shall honestly try to get some reading done real soon now.

Friday, July 12, 2013

Climbing to the top - Kidney Camp 2013

"Kidney" CAMP!

The FASEB Science Research Conference on "Renal Hemodynamics: Integrating with the nephron and beyond" took place last week at Vermont Academy in Saxton's River, VT. The meetings were previously called Summer Research Conferences, but they changed that to the quite strange "science research" that sounds more like a branch of philosophy to me.
Anyway, we still call it by its proper name: Summer Kidney Camp. It is a summer camp where spouses send their kidney physiologist halves to wear them out and enable at least a semblance of normal conversation during the rest of the summer. I'm guessing that doesn't work out as well as they hoped in much the same way as summer camp for kids don't.
The Kidney Camp is held every three years, and has a tendency to return to Saxton's River, even if it has been held in other locations once or twice. The main feature is the afternoon-break where we do important sciency stuff, like sitting in the grass, playing softball, football (proper football), basketball, and top rope climbing (which, by the way, is awesome). As far as I can tell most attendees only play sports once every three years for reasons unknown to science, and quite dangerous to be honest. The climbing was probably the safest activity.
The evenings are filled with more science. The fiercely competitive talent show, which was won by one of the supporting acts. The collaborative table tennis, and the very novel fussball table (rumor has it the last one broke three years ago) where any argument can be settled with a well timed spinning of the rods.
Then we have billiards, which makes you look better, but only until you pop the cue-ball off the table. Aaron, who is posing for illustrative purposes only, never did. I promise. Honestly.
In between these important scientific sessions there were some other stuff, where a lot of actual science was actually discussed. Some six to eight hours of lectures per day, and the best poster session in the field. Not only because it is the poster session with a bar that serves local micro-brewery beer, but also because the bar keeps people at the posters and everyone, even invited speakers, bring posters. Luckily it is three years to the next meeting so that I, and my liver, can recover.

Thursday, May 16, 2013

Patientsäkerheten kräver att alla data från kliniska prövningar publiceras

Öppet brev till de svenska Europaparlametariker som sitter i gruppen för Miljö, hälsa och livsmedelssäkerhet.
Kära Carl, Åsa, Christofer, Marit och Marita,
Jag skriver till er eftersom ni är med i Europeiska parlamentets grupp för miljö, hälsa och livsmedel som arbetar med frågan om publicering av data från kliniska prövningar. Jag är läkare och arbetar som ST-läkare i anestesiologi och intensivvård vid Akademiska sjukhuset i Uppsala och driver en forskargrupp som arbetar med högt blodtryck och akut njursvikt vid Uppsala universitet.  
Det är av yttersta vikt att alla kliniska prövningar publiceras, och att alla data från kliniska prövningar finns tillgängliga för metaanalys och jämförande forskning. Som medlemmar i Europeiska parlamentet har ni en unik möjlighet att föra den evidensbaserade medicinen ett stort steg framåt. Idag publiceras inte alla prövningar och bakomliggande data tillhandahålls inte för metaanalys av oberoende forskare.
Detta är oacceptabelt från ett patientsäkerhetsperspektiv eftersom läkare kan föreslå suboptimala eller rent av felaktiga behandlingar om de inte har tillgång till all information. 
Det försämrar europas möjlighet för forskning och utveckling genom att forskare i onödan gör om prövningar som redan gjorts bara för att de aldrig publicerats.
De patienter som ställt sig till förfogande för forskningen har en förväntan att deras uppoffring skall leda medicinen framåt. Genom att tillåta att data från kliniska prövningar undanhålls bryts patienternas förtroende för den kliniska forskningen. 
Publiceringskravet bör gälla alla kliniska prövningar för alla mediciner som säljs, oavsett om dessa är nya prövningar eller tidigare prövningar som aldrig publicerats. Om gamla prövningar tillåts förbli opublicerade kommer fortfarande majoriteten av de mediciner som används idag att ha okompletta data. 
Ni kan hitta mycket mer information på sidan 
Tack för att ni tog er tid att läsa detta och för att ni ställer er på patienternas, medicinens och forskningens sida i denna avgörande fråga för den framtida folkhälsan och medicinska utvecklingen.  
Ni som läser detta kan också skriva till era EU-parlamentariker. Deras e-postadresser hittas på 

Sunday, April 14, 2013

Renovating Jigoro Kano

Most judo clubs have a picture of the founder, Kanō Jigorō (28 October 1860 – 4 May 1938), close by the practice area. It is supposed to hang on the front wall. That is, the wall you face when entering the dojo, called the shōmen (front wall), or kamiza (high seat). The latter because before the advent of the picture that was where the head of the dojo would sit, and over-see practice (As in the below illustration by Shuzan Hishida).
In Bergen the picture had gone missing, and in Uppsala it is a framed but dilapidated poster. Anyway, I decided to get a new one, but quickly found out that it is all but impossible. As a photographer, and, if I say so myself, not a bad printer, my next thought was to find a picture online and print it. This is the story renovating a scan of an old Jigoro Kano portrait for printing. Luckily, by Japanese law any photographs taken before 1946 are part of the public domain (or that is what Wikipedia says).

When working with a picture you obviously want to start with the highest possible quality and resolution, and with a bit of work I found this rather good scan at 3543x4375 pixels (click on the picture to go to the original URL).
It is only a j-peg but with that kind of resolution you can do a lot without destroying it. This is good because there was a lot to be done. There are scratches that seem to be from the original photograph, including one prominent on his left eye-brow. There are some blotches on the background, and I do not want the text or the old name-badge. Finally, it is made from an old tinted photograph, and I don't like the tint.
So, I loaded the image into the old editor, i.e. Adobe Photoshop, and cleaned it up. I tried to upload the actual TIFF to Wikimedia-commons, but that didn't work so I have just uploaded the final j-peg. If I find another place to put the layered file I will, and then you can easily adapt it to your needs. It prints quite well up to A3.

Monday, February 11, 2013

Winter-meeting in Oslo

The Norwegian Hypertension Society held its bi-annual scientific meeting in Oslo last week. It was a long time in planning. We set the place and date about two years ago. Sent the first announcement in the spring of 2012 and the call for abstracts in September. Then, at the very deadline, the abstracts and registrations start to trickle in. As with all meetings, we pushed the submission-deadline back a week just to allow people without basic planning skills with pressed schedules to join the meeting and present their data. Then, in as little time as possible, all the abstracts have to be formatted into a program, and session-chairs has to be found and matched so that they have an interest but aren't speaking themselves.

Anyway, we got some 17 free communications, varying from experimental physiology to international research politics, but with a heavy focus on epidemiology and clinical research. There were a couple of talks on the recently very hot topic of renal sympathetic denervation for treatment-resistant hypertension (more on that in another post), some interesting sub-group analyses from the LIFE and SCAST studies, and follow-ups on the now 40-year-old Oslo-Ischemia-Study. More of the program at the society home-page.
In addition, we had two invited lectures on statistics in clinical research. The first on how to develop and validate prognostic models by Ingar Holme, and the second on over-adjustment bias in multiple regression models held by Knut Liestøl. It was a useful repetition of the uses and pitfalls of these two very similar kinds of models that require very different study-designs and give very different information in the end. A common problem is that one tries to get etiological information from prognostic research, i.e. treating a risk-factor as a cause for the chosen end-point even though the observational design makes that impossible. The converse is equally common, i.e. trying to infer prognostic information from etiological studies, such as clinical trials, where the highly selected population makes general conclusions very suspect.

All told, it was a very successful meeting, well worth the time both for planning it, and attending.

Sunday, February 10, 2013


The recent popularity of the up-goer five editor (check out the #upgoerfive hash on Twitter) pin-points an important point in writing: It's bloody hard to express a coherent thought in science without any specialised words. And I don't mean jargon or strange abbreviations but words like function, vessel, pressure, kidney and medicine (This point is made much better by the Center for plain language).

However, trying makes for a good bit of fun. The original fun was had by the brilliant Randall Munroe at when he reproduced a technical drawing of the Saturn V rocket with explanations that only included the 1000 most commonly used words. This excluded the use of "saturn" "V" and "rocket", so it was called the Up-goer five. Now, Theo Sanderson has created an editor that tells you when you have used a word that is not among the 1000 most used words. Here is my attempt to explain kidney function and the effect of hypertension induced injury on blood vessel and kidney function.
My job is to understand how the body parts that make piss work, and why they get hurt by the force that the heart makes when it forces the blood around in the body. In the body there are two blood-to-piss-body-parts. They work by making piss out of blood using many small blood-cell-catch-things so that the blood cells stay in the body. Then the blood-to-piss-body-parts take up most of the water again so that the piss becomes strong, and the body can save water. The blood-cell-catch-things use the force-of-the-heart to push water out of the blood. 
However, the smallest of the blood-roads and the blood-cell-catch-things are not strong, and can be hurt by the force-of-the-heart. In the long run this hurts the blood-to-piss-body-parts, and make them stop working. Before they stop working they work less well for a long time. During this time they are easier to hurt in other ways. One important way is when the force-of-the-heart becomes too low, often because of lost blood, and the blood-to-piss-body-parts get too little blood. Too little blood, and too low force-of-the-heart makes it hard to push water out of the blood to make piss. You then get too much piss in your blood which makes you sick. 
At the same time, air is carried by the red blood cells in the blood and used for doing work in the body. Too little blood to the blood-to-piss-body-parts gives them too little air, which they need in order to take back water from the piss. When the force-of-the-heart is low they need to take back even more water than usual to keep more water in the blood and keep the force-of-the-heart normal. This makes the blood-to-piss-body-parts use more air even though less comes to them. Since the cells that make up the blood-to-piss-body-parts need air to live, too little air hurts them and some of them die.

In a blood-to-piss-body-part that has been hurt by too high force-of-the-heart a sick with too low force-of-the-heart hurts more than in a well blood-to-piss-body-part. This means that for each earlier hurt the next hurt will hurt more and lead to blood-to-piss-body-parts that do not work at all faster and faster.

Too high force-of-the-heart hurts the blood-to-piss-body-parts by hurting the blood-roads first. This hurt changes how much blood passes the blood-cell-catch-things, and how much water is taken back to the body from the piss. Doctors can keep the blood-to-piss-body-parts from getting hurt by giving doctor-stuff that makes them work less hard and by keeping the force-of-the-heart normal. When the blood-roads have been hurt a lot it is hard to save the blood-to-piss-body-parts. Is important to keep the force-of-the-blood normal as much as possible.
If you want to read some other examples go to Ten Hundred Words of Science. Lots of fun for everyone.

Saturday, February 02, 2013

Speech impediment - Locale in R under OSX

My R-installation developed a language problem ("L" is a statistical ploglamming language). The startup message, all errors and system messages started appearing in German. I do speak German but it was still quite annoying. This ended with a work-around that I published previously in a post about R-startup scripts. I have finally figured out what causes the error. My Language & Text settings for language were as follows:
  1. British English 
  2. Swedish
  3. Norwegian
  4. Danish
  5. German 
  6. French 
The problem lies in using the British English locale. I use it because I hate when all programs always correct my excellent spelling from Proper English™ to American. R does not have a locale for British English, nor for Swedish, Norwegian or Danish. So, to R, the locale priority list actually looks like this:


    2. German 
    3. French
So, understandably it goes for what it knows. The solution is to extend the list and put a standard English locale high up:
    1. British English
    2. English 
    3. Swedish
    4. Norwegian
    5. Danish
    6. German 
    7. French