A rural virologist

A rural virologist http://www.theotokos.co.za/umtata/index.php The story of a rural virologist en http://backend.userland.com/rss092 <![CDATA[What is the past participle of bullshit?]]> bullshitted" today and it got me thinking about whether or not it's a transitive verb, and what the correct past participle would be. UK English has the past tense and past participle of shit as shat, but in Americanese it's shit in the past tense/participle as well. Bullshit as past tense and past participle just doesn't sound good, so Americanese is out. Bullshat ... doesn't sound good either. But, as far as I can recall, there are no, or few, English words ending with "t" that have their past tense ending in "ed", so I think this needs to be made a formal exception to the rule, and bullshitted recognised as the correct spelling.

Actually it seems to be - see the Wiktionary entries for bullshitted and bullshit. However, Google also lists 86000 hits for bullshat, and only 34000 for bullshitted, indicating that the former is more popular. Quite possibly because the Internet may have more sites written in or influenced by Americanese.]]> http://www.theotokos.co.za/umtata/post/index/60/What-is-the-past-participle-of-bullshit <![CDATA[Quality assurance vs quality control]]>
Good question.

The answer is, in English, nothing. The two are synonymous phrases. They have, however, been appropriated by bureaucrats to mean two different things in bureaucrat jargon that has infected countless poor individuals around the world for decades.

The terms also lack an important element - a real adjective. Good quality? Bad quality? There are plenty of organisations who do their best to maintain bad quality in their services.

See http://tinyurl.com/Quality-crapspeak for more on the bureaucrat usage.
]]> http://www.theotokos.co.za/umtata/post/index/56/Quality-assurance-vs-quality-control <![CDATA[Milwaukee Rabies Protocol]]> latest ProMed reports a case of a Brazilian boy who survived rabies. Like all previous survivors except one, he received vaccine as prophylaxis, but prophylaxis was incompletely administered (no immunoglobulin.) Apparently unlike the previous survivors, the virus was isolated from the patient. He was treated with the Milwaukee protocol first tried on the non-vaccinated girl in Wisconsin who survived. To what extent this is a result of the protocol is unclear - rabies after failed prophylaxis appears to have a higher survival rate, especially for bat rabies.

The ProMed report [22 Nov 2008] - Rabies, human survival, bat - Brazil (02)

Milwaukee Protocol 2.1 with its checklist can be obtained at the Children's Hospital of Milwaukee Rabies Registry page.

A few articles referenced in the protocol or the ProMed article or discussing the protocol:

Jackson AC. Rabies: new insights into pathogenesis and treatment. Curr Opin Neurol 2006;19:267-70.
PubMed link | Journal link

Wilde H. Failures of post-exposure rabies prophylaxis. Vaccine 2007;25:7605-9. Epub 2007 Sep 14.
PubMed link | Journal link

Jackson AC, Warrell MJ, Rupprecht CE, et al. Management of rabies in humans. Clin Infect Dis 2003;36:60-3. Epub 2002 Dec 11.
PubMed link | Journal link

Willoughby RE Jr, Tieves KS, Hoffman GM, et al. Survival after treatment of rabies with induction of coma. N Engl J Med 2005;352:2508-14.
PubMed link | Journal link

Hemachudha T, Wilde H. Survival after treatment of rabies. N Engl J Med 2005;353:1068-9.
PubMed link | Journal link

Jackson AC. Recovery from rabies. N Engl J Med 2005;352:2549-50.
PubMed link | Journal link

Hu WT, Willoughby RE Jr, Dhonau H, Mack KJ. Long-term follow-up after treatment of rabies by induction of coma. N Engl J Med 2007;357:945-6.
PubMed link | Journal link

Wilde H, Hemachudha T, Jackson AC. Viewpoint: Management of human rabies. Trans R Soc Trop Med Hyg 2008;102:979-82. Epub 2008 May 16.
PubMed link | Journal link

Human rabies--Indiana and California, 2006. MMWR Morb Mortal Wkly Rep 2007;56:361-5.
PubMed link | Journal link

cave canem? cave etiam vespertilionem!]]> http://www.theotokos.co.za/umtata/post/index/55/Milwaukee-Rabies-Protocol <![CDATA[Bullshit Bingo]]>
Learners - they are really pupils
Strategic - my arse (for Americans who don't speak English, "ass" refers to a donkey)
Value-added - like a tax
Quality - is a "quality item" of good or bad quality???
Service delivery - an excuse for bad service
Niche market - a market in a corner
Drill down - for oil???
Comprehensive - full of it
Project manager - he manages projects
Fixed-dose - I have never prescribed a variable-dose tablet!
Grass roots - where we find garbage, snails, and other crap
Culture - the culture of crapspeak is a niche market that adds value to strategic learners

Useful items to include in a game of Bullshit Bingo in your next meeting.

For those who don't know what Bullshit Bingo is, it's a form of Bingo where you have a card with words or phrases instead of numbers, and then wait for those words/phrases to be used in meetings or speeches. When you hear them, you cross them off. Once you have a full line (across, down, or diagonal) crossed off, you shout "Bullshit!" and you've won.

Here's an example of a Bullshit Bingo card:

You can make such cards (each person should get a slightly different card, so not everyone has the exact same words in the same positions) and distribute them at your next meeting.]]> http://www.theotokos.co.za/umtata/post/index/54/Bullshit-Bingo <![CDATA[Kitten with chicken jelly?]]>

Friskies is one of the things my babies love. They don't know what's in it. Nor do I.

]]> http://www.theotokos.co.za/umtata/post/index/53/Kitten-with-chicken-jelly <![CDATA[Tuna mayo sandwich expiry date]]> Tuna mayo sandwich expiring in 2010 AD

]]> http://www.theotokos.co.za/umtata/post/index/52/Tuna-mayo-sandwich-expiry-date <![CDATA[HIV prevalence drop - fact or fiction?]]> 2007 National HIV and Syphilis Prevalence Survey [PDF] aka Antenatal Survey.

It appears that the new stats have been produced using a new method~~ology~~ to work out its conclusions.

Two people who know what they're talking about when it comes to these stats wrote a letter to the SAMJ, which can be found here [PDF].

The new weighting gives rise to some absurd results. For example, the prevalence in the Western Cape, which previously had the most rapidly growing epidemic, albeit from a low base, apparently fell from 15.1% in 2006 to 12.6% in 2007. This while, apparently, prevalence fell in only two districts, and in both cases by less than 1%, and in the presence of a significant roll-out of life-preserving treatment which would, other things being equal, lead to an increase in the numbers of infected women in the province.

Rob Dorrington, David Bourne. Has HIV prevalence peaked in South Africa? – Can the report on the latest antenatal survey be trusted to answer this question? SAMJ October 2008, Vol. 98, No. 10

Reported here by IRIN:

After recalculating the 2007 figures, using the same method applied to the 2006 data, the authors estimated HIV prevalence among pregnant women at 29.4 percent. Antenatal prevalence figures are used in combination with other surveys and mathematical models to determine HIV prevalence in the overall population, but the revised figure suggests that the number of South Africans living with HIV has probably not declined. ...

Dorrington and Bourne conclude that "analysis of these data appears to be becoming increasingly beyond the skills of the Department of Health" and recommend that the government enlist the help of the broader scientific community to help interpret future figures on prevalence.

Reported here by the Treatment Action Campaign.

The Minister of Health has touted the drop in HIV prevalence as a success. Her claims must be treated with scepticism. Nevertheless, a slight increase in prevalence would not indicate a worsening HIV epidemic. Prevalence measures the total number of HIV positive people at a specific time. A decrease in prevalence for the whole population can only occur if more people with HIV die than become infected ...

At this point in the HIV epidemic, the key measure of HIV prevention success is incidence, i.e. the rate of new infections. ...

TAC calls upon the South African National AIDS Council (SANAC) to assist the Department of Health with the analysis and interpretation of the results of the antenatal survey.

TAC calls upon the Department of Health to release the details and rationale for the methodologies used to calculate provincial and national prevalence from district data for its 2007, 2006 and 2005 antenatal prevalence studies.

A note on the correct use of the terms "method" and "methodology" which do NOT mean the same thing:

A fondness for big words isn't always accompanied by the knowledge of their proper use. Methodology is about the methods of doing something; it is not the methods themselves. It is both pretentious and erroneous to write "The architect is trying to determine a methodology for reinforcing the foundation now that the hotel on top of it has begun to sink."

Source: Common Errors in English

Politix.]]> http://www.theotokos.co.za/umtata/post/index/51/HIV-prevalence-drop--fact-or-fiction <![CDATA[How to kill better]]> Ethical Implications of Modifying Lethal Injection Protocols"

Courts in the United States have historically judged execution methods against "evolving standards of decency," and have prohibited punishments that involve "the unnecessary and wanton infliction of pain," or more recently the "substantial risk of serious harm".

Harm? Isn't death "serious harm"?

"The intravenous delivery of an anesthetic, a paralytic, and potassium chloride in lethal injection protocols is intended to cause a painless death, which likely accounts for its use in 930 of the 1,100 executions in the United States from the re-establishment of the death penalty in 1976 to May 6, 2008 ..."

We no longer have the death penalty in South Africa. And when we did, it was never the electric chair. Imagine load shedding during an execution?

Under all accepted ethical guidelines, including the Common Rule, participation of research subjects must be free and not subjected to undue influence or coercion. Finally, while some lethal injection studies could be considered minimal or no risk (electrocardiogram monitoring, post-mortem sample collection) others, including the addition or omission of drugs and altering of drug doses and sequences, seem to present substantial risk. Indeed, the risk of extreme pain and suffering is at the heart of the current lethal injection debate.

BTW, the myth that if someone fails to die during an execution he/she gets freed is just that - a myth.]]> http://www.theotokos.co.za/umtata/post/index/49/How-to-kill-better <![CDATA[Crappies, anyone?]]> smut was killing the sugarcane in Australia. Now bacteria are killing the crappies near Ashby, MN, USA.

Most crappies were small, "but 10- to 15-inch crappie were also observed."

It's not all bad news:

"Assuming good numbers of adult crappie remain, they'll be very successful in producing lots of young crappie in 2008 to fill the void ..." - ProMED-mail, 15 Sept 2007 ]]> http://www.theotokos.co.za/umtata/post/index/47/Crappies-anyone <![CDATA[Warning - headless snakes can bite]]> Headless Snake Bites Hapless Man

In fact, "decapitated snake heads are dangerous for between 20 and 60 minutes after removal from the body of the snake," Jeffrey Suchard of the Good Samaritan Regional Medical Center in Phoenix told SciAm's own Steve Mirsky earlier that year. So remember: wait an hour before handling a dead snake.

So says Scientific American, which also refers to the NEJM article:

Dead rattlesnakes can bite? Mayo Clin Health Lett 1999;17:4.
PubMed

Suchard JR, LoVecchio F. Envenomations by rattlesnakes thought to be dead. N Engl J Med 1999;340:1930.
PubMed
Excerpt at NEJM

So be careful. Don't be bitis. ]]> http://www.theotokos.co.za/umtata/post/index/42/Warning--headless-snakes-can-bite <![CDATA[Puff the Magic Adder]]>
Yesterday, a baby puff adder was found in Jeevs' garden. Very cute, and about 25cm long (an estimate - he didn't stretch himself out for us.) Species name: Bitis arietans - you have to be careful because they bitis! Apparently quite common in Mthatha.

He was very cold, and hiding under a box, safely stowed away in the back of a bakkie. We put him in a smaller box, and took him inside. He took a liking to one of the pieces of the box he could hide in - maybe just because we were inspecting him and he didn't like that.

Luckily he wasn't in the mood for biting, although we didn't touch him while he was able to get a nip in.

Here is is getting into his little corner:

A close up:

Even more:

All the way in:

People here are terrified of snakes ... this one is sweet, though, and well behaved. He's quite safe to look at if you're careful - snakes don't carry viruses that can transmit to humans. ]]> http://www.theotokos.co.za/umtata/post/index/41/Puff-the-Magic-Adder <![CDATA[Driving skills in Umtata]]>
I think a very high percentage of drivers here either have no licence, or they bought it. If you're a government official, or work for one, the rules of the road don't apply to you, as the newspapers recently pointed out. But they don't apply to anyone else either.

The yellow lane is a passing lane for taxis in many parts of the country; here, that holds true, but the oncoming lane is also a passing lane for taxis here. As soon as it's dark, and you can no longer see the lines on the road, they become irrelevant, as I discovered in yesterday's power failure (almost as common as roads here in Umtata.)

When I had nearly reached my destination, driving in the middle lane of two, with cars passing me in the parking spaces on my left, I luckily didn't know whether I needed to turn left or right, so I turned left and parked. Had I tried turning right, I'd have ended up in the funniest traffic jam I've seen.

In normal society, if the traffic lights don't work, they should be treated as a 4-way stop. In Umtata, you just don't stop. Other traffic has to wait for you. It's a bit better at real 4-way stops. There you just have to push your way into the intersection. If you're second in line, you can get through without waiting your turn simply by going through on the tail of the car in front of you. Generally, the unwritten rule here is that if the car entering the intersection hasn't yet obstructed your path, you can still enter and go.

The traffic jam was a perfect example of how rush hour traffic in Africa works. Everyone has the right of way, everyone can go first, so everyone does. And by refusing to allow anyone else right of way, it ends up as a huge mess. Nobody can move. Eventually the police arrived and I assume they sorted it out, after solving a dispute between a car and a Fidelity Guard van whose noses were almost touching, each refusing to move for the other one. I left after getting a few photos - not ideal ones, in the dark - with my cell phone's camera.

A bit blurred, but you can make out the green van with Fidelity on the side.

Some cars had opened their doors. The drivers had to explain to those who didn't have right of way how they should drive.

Will Africa ever learn? ]]> http://www.theotokos.co.za/umtata/post/index/36/Driving-skills-in-Umtata <![CDATA[HIV treatment in a warzone]]> HIV treatment in a conflict setting: outcomes and experiences from Bukavu, Democratic Republic of the Congo, by Heather Culbert et al in PLoS Medicine, 2007 May;4(5):e129
PubMed link
Article on PubMed Central
Article on PLoS Medicine

Patient 1
Followed in the clinic since 2002, on ART since December 2003. Lives in Rwanda.

When the fighting started, I thought that it was the end of our lives. I had only treatment for three days and five days of security. I had interrupted my treatment for two days when another patient arrived with the treatments sent by MSF. I was afraid it was the end of my life because more than just the [lack] of medications, I was very sick and I had to be hospitalised with fever and vomiting. It is very important to have the treatment.

Patient 2
Followed in the clinic since May 2003, and on ART since December 2003.

I heard gun fire all through the night. When I had only five pills left I lost my appetite and felt desperate... but despite the uncertainty I continued to take my treatment at the correct hour... When I had only one pill left I had the courage to go out and seek some more treatment. I went to see [my] nurse [at her home] who informed me that she would be able to distribute ARVs; with that I had a month’s worth of treatment. If we have to give up this treatment we will return to how we were at the start, sick.

Sad, very sad. ]]> http://www.theotokos.co.za/umtata/post/index/35/HIV-treatment-in-a-warzone <![CDATA[Australian smut]]>
And no, it has nothing to do with sheep.

Pictures of this smut can be seen here and here.

The full report is on ProMED-mail. ]]> http://www.theotokos.co.za/umtata/post/index/34/Australian-smut <![CDATA[Technovirology in action]]>
Jeevs' son, Reshlan, had a project for medical school on a flashdisk, and every time it was plugged into a PC with antivirus software, that file got deleted. The file was a Word document. The virus had inserted executable code in the beginning of the file, and renamed it with the extension SCR. SCR files are usually screensavers.

The logical person to ask for help is ... the virologist.

The virus was W32.Rungbu, as named by Norton.

Here I describe how I chopped the virus out of the file, and got back the original Word document.

PLEASE NOTE: this is not for the faint hearted, or for anyone who, like me, doesn't really know what he's doing. You risk your computer becoming infected, and losing data. What I describe below is not something you should try at home.

First, I backed up my registry, and turned off System Restore, and then inactivated my antivirus software.

I copied the infected file.scr onto my hard drive. Then I renamed the infected file so it had a TXT extension, and opened it in Notepad. It looked like this:

Lower down, some of the text contained in the Word document was visible. I didn't know what to do ... so I tried various things, none of which worked. Forcing the file.scr to open in Word or Wordpad didn't work - it had non-Word header information that Word couldn't interpret. I tried chopping off the top part of the document, including everything between the start of the document and the end of the code inserted by the virus. I tried chopping out the part of the document that was clearly Word, and placing it into a document from which I removed that document's section from that position onwards. For this I was using Notepad, and was probably saving it in some way I shouldn't have saved it - or maybe I shouldn't have been saving it at all in Notepad. None of the final products opened in Word.

In the process I followed above, I discovered that all the Word documents I checked began the same way. I already knew that this was the case with GIF, JPEG, PDF, RAR, and ZIP files, so I was expecting that. The following three images show how three different Word files began:

I've highlighted the sequence common to all the files.

But, as I said above, deleting everything before that sequence and saving the result using Notepad produced a file that Word couldn't open.

Then I thought of using a hex editor to delete the infected section. I used a fairly simple programme called 1Fh Binary+Hex Editor 1.07.

By searching for the specific sequence that the other Word documents began with, I found out that the first 46592 bytes of the file were something else. This is what it looked like:

The B600 is the hexadecimal version of 46592, which I could have calculated by hand, but was too lazy, so I used HexDecBin 1.0 to do it for me:

I decided that using 1Fh to space over the extra 46592 bytes would simply take too long. So I thought that maybe splitting the file into pieces, in such a way that the extra piece would be separated from the rest, might allow me to piece the file back together without that extra piece.

For this I used GSplit 2.0. I simply split the file into pieces 46592 bytes in size - so that the first piece would be the the entirety of the extra piece, presumably the virus, and not contain any authentic piece of the original Word document. I also set GSplit to omit headers to the pieces that it split the file into, to not create an executable file that would piece them back together again, and, in case it affected anything, deleted the code set to give the pieces a unique ID.

Then I split the file - 35 files resulted, namely disk1.gsd, disk2.gsd, ... disk35.gsd.

I checked disk2.gsd, and, not surprisingly, it began with the sequence that started all the other Word files.

I then ran a batch file to unite all the pieces except the first. It looked like this:

copy /b disk2.gsd+disk3.gsd cow.gsd
copy /b cow.gsd+disk4.gsd cow.gsd
copy /b cow.gsd+disk5.gsd cow.gsd
...
copy /b cow.gsd+disk35.gsd cow.gsd

The /b was simply because I expected it to be a binary file and not an ASCII file like a text document. (Probably something to do with Notepad saving it in a way that Word couldn't interpret as a Word file.)

I then renamed cow.gsd to cow.doc ... and tried to open it in Word. And there was the original, opening fine as a normal Word document. (It had another error in it, and wouldn't show page 48, but that I converted to a PDF and the PDF back into Word, and recovered the text that way.)

And that is amateur technovirology in action, as performed by a clinical virologist. Viruses are indeed fun! ]]> http://www.theotokos.co.za/umtata/post/index/32/Technovirology-in-action <![CDATA[The Dead Movies]]> George Romero's Dead movies:

Night of the Living Dead [1968]
Dawn of the Dead [1978]
Day of the Dead [1985]
Land of the Dead [2005]

Diary of the Dead, for release in 2007, is a 5th, but not a sequel to Land of the Dead, as it takes place at the during the initial outbreak of the zombies that occurred in Night of the Living Dead.

Remakes of these movies by other directors:

Night of the Living Dead [1990]
Dawn of the Dead [2004]
Night of the Living Dead 3D [2006]
Day of the Dead [2007]

And then of course there's Shaun of the Dead [2004], a spoof of the above, not by George Romero. See also Night of the Living Bread [1990].

Wikipedia has a good explanation of which are Romero movies, which are Russo movies, and which are non-Romero "sequels" and related and unrelated movies, such as unofficial non-Romero non-Russo sequels Day of the Dead 2: Contagium and Zombi 2.

The original Night of the Living Dead was co-written by George Romero and John Russo. Romero sequels are "Dead" movies and Russo sequels are "Living Dead" movies.]]> http://www.theotokos.co.za/umtata/post/index/30/The-Dead-Movies <![CDATA[Anna Vissi blog]]> this means:

Και ενώ η πε�?ιοδεία της Άννας στην Αμε�?ική συνεχίζετε ανακοινώθηκε ότι η Άννα Βισση στις 12 Μάιου 2007 θα δώσει μια συναυλία στο Sun City / South Africa.

Probably something to do with Άννα Βισση coming to Sun City in May.

They linked to me ... so here's the Anna Vissi blogspot. ]]> http://www.theotokos.co.za/umtata/post/index/29/Anna-Vissi-blog <![CDATA[The usefulness of boxes and other junk]]>

This is some sort of crate packing support device that I have turned into a shelf for my DVDs and CDs, and maybe a few books when I get more of those unpacked.

Very fashionable. ]]> http://www.theotokos.co.za/umtata/post/index/26/The-usefulness-of-boxes-and-other-junk <![CDATA[Congratulations Estrelita!]]>
On 28 March, she was awarded an Exceptional Achievers Award.

The Pretoria News (which we don't get in Umtata - my mom e-mailed me the article) said:

University of Pretoria spokesperson Stella du Plessis said: "The university is extremely proud of those people who are responsible for establishing and maintaining its reputation as the leading research university in the country."

The article can be read here.

I also know Prof Louis Nel, Prof Brenda Wingfield, and Prof Mike Wingfield.

Congratulations! ]]> http://www.theotokos.co.za/umtata/post/index/24/Congratulations-Estrelita <![CDATA[TB is NOT a virus!!!!!]]> Mycobacterium tuberculosis and related bacteria are bacteria, NOT viruses.

The following are also not viruses:

malaria
typhoid
tick bite fever
syphilis
gonorrhoea
cats and dogs

"More hospitals to treat TB virus" published on 14 March 2007 in The Mercury (a newspaper) should have a better headline.

Some snippets:

She acknowledged that the department had been grappling with the challenge posed by MDR TB and XDR TB.

I am sure they are ... it's quite a problem. The local stats sound quite scary.

MDR TB and XDR TB result from the failure of patients to take their treatment as directed when diagnosed with tuberculosis.

Hmmm ... do they mean that MDR and XDR TB in a patient result from that patient's treatment failure? MDR often yes, and I'm not an expert on the genetics (I'm a virologist, and TB is NOT a virus) but I think the jury is still out on XDR TB, and there is some evidence that XDR infections are usually caused by an XDR strain infecting the person.

"We are not satisfied with the budget allocation because of the high prevalence of HIV and TB in the province, and the move by the Treasury to reduce the allocation for revitalisation funds will impact negatively on infrastructure development," said Nkonyeni.

We definitely need more money to fight HIV and TB in this country. ]]> http://www.theotokos.co.za/umtata/post/index/23/TB-is-NOT-a-virus