Combining PubMed RSS feeds with Bloglines to conveniently survey new developments

A Medlogs entry pointed me to an interesting new PubMed [1] feature -- syndication!

(1) Run your search in PubMed.
(2) Select RSS Feed from the Send to menu.
(3) Click Create Feed and copy the XML icon into your RSS Reader.

I of course had to try this out. Years ago I embedded (now broken) search links in web pages, but one runs into the notification problem. It's very boring to keep clicking on a link and finding nothing has happened. Syndication is a vastly better model.

I tested this out an old search I've long been interested in: the genetics of berry aneurysms and screening for subarachnoid hemorrhage. I logged into PubMed and set up a search, then followed the directions above; I limited the search to Bloglines, my syndication (RSS, Atom) web client, and added this URL as a feed to a new folder called "PubMed searches" (you can copy this URL and try this in your favorite feed client yourself.)

On my first view I got 41 hits. After reviewing those the list was empty (as it should be), but as literature emerges that list should refresh. One wonders how the PubMed server will handle the transactional burden, since these unique searches may not scale well to thousands or millions of users. For now, however, the PubMed RSS and Bloglines combination is the neatest thing I've seen in this domain since Grateful Med.

If you'd like to see how this looks, without doing all of the above work, visit the public view of my bloglines list and click on the PubMed folder. It is very cool. You can also see the searches on my (hidden) blogroll page.

I guess I'll have to update that old, old, page of mine. (11/17/05 - I did. The page was over 6 years old.)

[1] Old dogs remember MEDLINE, MEDLARS, Grateful Med, etc. Really old dogs even remember the vast printed volumes of Index Medicus, and using early terminals to send query strings to Bethesda. Creak, creak ...

Interesting alterantive to mass quarantine -- focus on the high-risk super spreaders ...

Scientific American has a brief note on a fascinating topic. I did some simulation work during my last degree (10 years past now!) and I suspect the simulation community has been exploring this for awhile. Public health, of course, has been thinking about this since 'Typhoid Mary'; more recently one sociable male flight attendant was once considered to have been a sort of "super spreader" early in the HIV epidemic.

It turns out computer modeling of epidemics suggests an alternative strategy to mass quarantine:

Science & Technology at Scientific American.com: Study Assesses Impact of "Superspreaders" of Disease

... There are two ways for a population to protect itself: either everyone can act to reduce their chance of transmission--for example, by staying at home, which can throttle a country’s economy--or authorities can identify those most likely to be superspreaders, and focus their vaccination and isolation efforts on them. --Kaspar Mossman

In Minnesota we have recent experience with a young Amish child who is, due to an immune defect, a "super spreader" of polio [1]. The concept of "super spreader" has thus been in the news here. I suspect the simulation study is looking at more subtle super spreaders however.

If we do find reasonable tests to identify super spreaders, we would be well advised to think about compensating them for the inconveniences (or worse) a selective quarantine would create. As a way to manage the coming wave of epidemics [2], however, this is well worth researching.

[1] The combination of "super spreader", Polio, and unvaccinated community is potentially explosive, but fortunately our republican governor has not quite finished dismantling Minnesota's still excellent public health infrastructure.

[2] As humanity simultaneously travels more, congregates more, expands into Africa, and reproduces more, we become an ever richer petri dish for novel infections.

iPod over all -- 10/10 on Amazon

Amazon.com: Early Adopters - computers list has an iPod in each of the top 10 slots.

The audio and video list has in each of its top 10 slots ... iPods.

I think Amazon only sells 10 varieties of iPod.

That's astonishing.

Gordon's Tech: Replicate the experience of 19th century phone service

Gordon's Tech: Replicate the experience of 19th century phone service: "Thanks to the miracle of modern technology, one can combine Skype VOIP, a modern laptop, a wireless LAN and a USB full duplex speakerphone to recreate the turn of the (prior) century experience of yelling 'HELLLLOOOO, CAN YOU HEAR ME??'."

A quick preview on the next thing to blow your world apart

Do it yourself. Almost. ... Dan's Data provides a quick update on the state of the art in 3 dimensional "printing". As in download the specs, run the illegal hacking software, and print yourself an anonymous encrypted cell phone. Ok, so we're not quite there yet. Soon though.

Alvin Toffler didn't know the half of it. (Or did he? Read the wikipedia article ...)

All your bases belong to Google: the beginning of the end

The net shook this morning as Google dropped the hammer:

Official Google Blog: First Base

Right now, there are two ways to submit data items to Google Base. Individuals and small website owners can use an interactive user interface; larger organizations and sites can use the bulk uploads option to send us content using standard XML formats.

Rather than impose specific schemas and structures on the world, Google Base suggests attributes and item types based on popularity, which you can use to define and attach your own labels and attributes to each data item. Then searchers can find information more quickly and effectively by using these labels and attributes to refine their queries on the experimental version of Google Base search.

This beta version of Google Base is another small step toward our goal, creating an online database of easily searchable, structured information...

Meanwhile, in Redmond, insiders are dumping their shares ...

The initial version of Google Base is entirely public. Too bad, I'd have liked to create a private list of contact information for our cub scout troop. There doesn't appear to be any access restriction, it's very much designed to create public knowledge. Some of the templates they provide compete directly with Amazon, eBay, Craig's List and (above all) newspaper classifieds, but they've yet to provide commercial transaction services (that's next week). Other templates are for recipes, reference articles, course catalogs and other shared knowledge. It appears one can use XML structures to create one's own templates (vendors bidding for software projects?). The intersection between formally structured and emergent metadata is intriguing.

Elsewhere, Google writes "content providers who already have RSS feeds can easily submit their content to Google Base without requiring much additional work". This is the original vision of RDF metadata as first presented in Apple's mid-90s "Project X" and the more recent vision of the "Semantic Web".

Google Base is a component of potential web services. Google will use it, so will others.

Now we await the micro-commerce transaction system that will transform Google into a multinational financial powerhouse.

This is fun. Scary, but fun. A bit like inline skating downhill ...

The Economist is falling out of love with Bush

The Economist, a once great newspaper lately in decline, rediscovers some ghost of its historic spine. Emphases mine -- they do reveal a certain depth of feeling:

Torture | How to lose friends and alienate people | Economist.com

Nov 10th 2005
From The Economist print edition

The Bush administration's approach to torture beggars belief

THERE are many difficult trade-offs for any president when it comes to diplomacy and the fight against terrorism. Should you, for instance, support an ugly foreign regime because it is the enemy of a still uglier one? Should a superpower submit to the United Nations when it is not in its interests to do so? Amid this fog, you would imagine that George Bush would welcome an issue where America's position should be luminously clear—namely an amendment passed by Congress to ban American soldiers and spies from torturing prisoners. Indeed, after the disastrous stories of prisoner abuse in Abu Ghraib, Guantánamo Bay and Afghanistan, you might imagine that a shrewd president would have sponsored such a law himself to set the record straight.

But you would be wrong. This week saw the sad spectacle of an American president lamely trying to explain to the citizens of Panama that, yes, he would veto any such bill but, no, “We do not torture.” Meanwhile, Mr Bush's increasingly error-prone vice-president, Dick Cheney, has been across on Capitol Hill trying to bully senators to exclude America's spies from any torture ban. To add a note of farce to the tragedy, the administration has had to explain that the CIA is not torturing prisoners at its secret prisons in Asia and Eastern Europe—though of course it cannot confirm that such prisons exist.

... Although Mr Cheney has not had the guts to make his case in public, the argument that torture is sometimes justified is not a negligible one. Khalid Sheik Mohammed, presumed to be in one of the CIA's “black prisons”, is thought to have information about al-Qaeda's future plans. Surely it is vital to extract that information, no matter how? Some people think there should be a system of “torture warrants” for special cases. But where exactly should the line be drawn? And are the gains really so dramatic that it is worth breaking the taboo against civilised democracies condoning torture? For instance, Mr McCain argues that torture is nearly always useless as an interrogation technique, since under it people will say anything to their tormentors.

If the pragmatic gains in terms of information yielded are dubious, the loss to America in terms of public opinion are clear and horrifically large. Abu Ghraib was a gift to the insurgency in Iraq; Guantánamo Bay and its dubious military commissions, now being examined by the Supreme Court, have acted as recruiting sergeants for al-Qaeda around the world. In the cold war, America championed the Helsinki human-rights accords. This time, the world's most magnificent democracy is struggling against vile terrorists who thought nothing of slaughtering thousands of innocent civilians—and yet the administration has somehow contrived to turn America's own human-rights record into a subject of legitimate debate...

A diabolical use of Google Adwords

Dan, of Dan's Data fame, casually tosses this aside into a comment on strange Adwords adorning his site:

Dan's Data letters #154

Actually, of course, some people actually do click ads that contradict what a site is saying, and not always because they agree with the advertiser. If you're reading a page about how reprehensible anti-vaccination activists are, and find an ad-link at the bottom that says FREEMASONS USE VACCINES TO NEUTER CHRISTIAN KIDS, you might feel a strange urge to click it. Not only to revel in the craziness, but also to transfer some money from the crazies to the owner of the page on which the ad appeared.

Ooooohhh. That never occurred to me. I'm so naive. Heh, heh, heh ....

The Ownership Society and the evolution of Social Darwinism

Crooked Timber has some interesting comments on Barak Obama and John Edwards.

The Obama quote that caught my attention was his making the 'social darwinism' to 'ownership society' connection. I'd wondered when this would come up, I'm glad to see it emerge now. Just as Creationism 'evolved' into 'intelligent design', so too has 'social darwinism' evolved into 'the ownership society'. Kudos for Barak Obama for launching this meme.

CT also links to John Edwards. What did you think Edwards was doing? I'll bet you didn't know he's launched a guerilla war on poverty? Hmm. Dean and Edwards in 2008? They might get Jimmy Carter's vote. Four more years of Bush might make economic populism a winning solution.

Kaplan trashes Bush's new mantra: "I was wrong, but so were you."

I Was Wrong, but So Were You - Parsing Bush's new mantra. By Fred Kaplan is well worth the read. Point by point Kaplan walks through a recent Bush speech and exposes the fundamental lies in point by point detail.

Why such a pathetic attempt at deception? My guess is Bush long ago gave up on talking to anyone who might doubt him, now he's just fighting to keep his base intact. Their credulity is well understood.

How to Write a Complaint Letter - eHow.com

Makes sense to me: How to Write a Complaint Letter - eHow.com

Where we learned to torture -- from Maoist China

The NYT details how the US developed its torture methodologies. We took a program called "SERE" that was used to instruct military personnel on how to resist Korean and Vietnamese torture. We then inverted the methods to create our own torture program:

Doing Unto Others as They Did Unto Us - New York Times

...SERE methods are classified, but the program's principles are known. It sought to recreate the brutal conditions American prisoners of war experienced in Korea and Vietnam, where Communist interrogators forced false confessions from some detainees, and broke the spirits of many more, through Pavlovian and other conditioning. Prolonged isolation, sleep deprivation, painful body positions and punitive control over life's most intimate functions produced overwhelming stress in these prisoners. Stress led in turn to despair, uncontrollable anxiety and a collapse of self-esteem. Sometimes hallucinations and delusions ensued. Prisoners who had been through this treatment became pliable and craved companionship, easing the way for captors to obtain the 'confessions' they sought.

It's very American to learn from the best, and Maoist China drew on thousands of years of experience with torture. Our refined techniques are a credit to a long line of historic torturers. The next step will be to define a career path for the most capable torturers, perhaps one that leads to a cabinet level position and a presidential "Medal of Honor". Perhaps someone who will head the "Ministry of Comfort"?

PS. Where's Margaret Atwood these days?

The story of a man who couldn't read

Jacques Demers, a famed figure in hockey and in Quebec, recently revealed he cannot read. Actually, he co-authored a book about it. Reading of his achievements, and his ability to apparently conceal his disability, I wonder if he has some specific neurologic cause of his reading inability - beyond his limited educaton and traumatic childhood. It would be interesting to know of his children have had problems. The NYT article is well written and tells a remarkable tale.

What if the EU and UN declare Bush and Cheney to be international criminals?

Bush, Cheney and their administration probably violated a number of international laws in their outsourced torture operation. Now the investigations are underway.

Spain Looks Into C.I.A.'s Handling of Detainees - New York Times:

...Last week, related investigations were started by the European Union and the Council of Europe to look into reports of secret C.I.A. jails for terrorism suspects in Eastern Europe.

An inquiry seems likely by the United Nations' special rapporteur on torture, Manfred Nowak. Last week he said that if reports of the C.I.A.'s activities proved correct, then the agency was engaged in a 'systematic practice of enforced disappearance.'...

Wouldn't it be "funny" if Bush and Cheney were found to be war criminals, and could not travel to Europe for fear of arrest?

Unlikely of course. They're merely doing what most tyrants do, and the UN is full of tyrants. Most European nations have similar episodes of shame in their recent history. Still, it's good to know at least one investigation is proceeding.

The neoprene back wrap and other parts of John's acute back pain recipe

Most mortals have more than a few flaws in their design. By middle-age you know most of them. Among mine is a bad back, a familial disorder that first manifested 25 years ago when I body surfed into the shore of Huntington beach.

So beyond my mere medical experience, I have twenty years of personal experience with (mostly) non-neurological bad backs (the kind where something tears, there's bleeding, scarring and lots of muscle pain). As in drop to the floor and lie there trying to figure out how to reach the phone. Which is why I'll pass on some hard won knowledge today, with the canes at my side. Don't follow this advice without the approval of your physician; your back may differ. You might even have a serious medical problem, though most bad backs are like mine.

Here is what works for me, It's also pretty much what's in the current guidelines:

1. Cold packs. The miracle innovation here is the TRU-FIT Ice/Heat Back Wrap w/ Gel Pack. Stick a cold pack in it (you're supposed to use the cold packs designed for humans, not the frost-bite inducing packs for picnic units). Wear it. Rotate pack every 1-2 hours, so you need 3 packs. For me 2-3 days of continuous use is important. Diabetics and elderly need to be careful of cold damage. There is a weight related problem with cold packs. Fat is a great insulator (that's one of the reasons we deposit fat under our skin). The more fat you have, the less effective the cold pack is; it becomes harder to cool the deep tissues and restrict incoming blood flow. One might be tempted to use the picnic coolers (colder stuff), but you run the risk of necrosing superficial tissue, visit to the ICU, death, etc. America seriously does need a pill for obesity; I wouldn't mind one myself.

2. Canes. $22 at Walgreens. Swear by them. Good for getting off the floor and making it possible to ambulate fast. When you need to cough, you need the cane. I use two for 2 days typically, then 1 for a week or so.

3. Meds: tylenol and ibuprofen alternating for 2-3 days then as needed. Vicodin (tylenol + hydrocodone) if you have it is very valuable for the awful first night, but no more than 1-2 days of use. You need the Vicodin on hand; when this kind of back attack hits a trip to the doctor is inconceivable (way too much pain). By the time one can travel the Vicodin is no longer needed. I used to prescribe Flexeryl to patients and I suspect it works, but I don't use it myself.

4. Sleep: on a carpeted floor, maybe with one of those very thin inflatable outdoor camping mats. Not the inflatable beds, the mats used by serious hard core hikers. Keep extra cold packs in a nearby insulated container. Also meds, water bottle and, for men, a .. ummm ..."receptacle". You don't want to have to get up if you can help it!

5. Ambulation and exercise. There are religious wars around this; extension exercises are most popular now. I do whatever doesn't hurt too much and I walk as much as I can. I skate to relieve back pain, which is insane. However, if one can avoid falling, this works very well after day 3-4. A gym elliptical exercise machine is far safer and works in a similar fashion.
I start the gym, cane at my side, on day 3. Climbing stairs often works well for me, if the decent hurts a down elevator is handy. Basically if it hurts, I do something else.

Usually by day 5-7 I can do a fair bit of exercise. I don't run ever, but biking and skating can work. It if hurts I don't do it.

6. Course? Awful for about 12-24 hours. Bad for another day. By day 5-7, if no re-injury, feeling almost well. It takes 6 weeks to have a reasonably solid back. I try to avoid heavy lifting for 2-3 months but often do it earlier (heavy for me is 80lbs, I'm a wimp). If I'm exercising properly I've never hurt my back when lifting fairly heavy items properly (straight back lift). Sitting, on the other hand, is really tough on a back. I have an Aeron chair at work (legacy of startup days) and in the acute phase I lie on the ground part of the day, ambulate often, and do phone conferences while walking.

7. Prevention? It's all weight control and exercise, and a some basic back hygeine. Sitting is bad but unavoidable. Don't push things, even light things, bent over. I knew I was due for this episode because family obligations have messed up my exercise regimen. Weight training and stretching and aerobic non-impact. Running is a very bad idea for most bad backs.

The only new prevention thing I'm going to add is using the gel pack early when I've done something dumb -- before my back "goes out" in a big way. I'm hoping early action with ice, healing activity, and careful exercise will avert major ruptures.

Update 8/1/2010: Things got much tricker later. I changed my mind on what works.