Get a journal article through your library proxy quickly with Alfred 2

It is always a pain clicking on a link to a journal article only to hit a paywall. It’s doubly painful when I know I have institutional access via my library’s proxy server, but have to jump through hoops to get it: go to the library website, log in, copy and paste the article name or PMID into its PubMed search box, and finally download the PDF. Arduous, and—turns out—unnecessary.

Enter Alfred 2 workflows. Here’s a nice article I found on Twitter today. The NEJM link in the top right corner leads to an abstract, but I need a special archive subscription for the full PDF. No matter—I can just highlight the PMID and hit my special Alfred 2 keyboard combo:

Since I’m not already logged into the Welch library proxy, I hit a login wall. It’s nothing 1Password can’t solve, but you can also just type in your username and password yourself, like an animal.

And Bam! The ugly but magic button is where it should be. Your institution might have a prettier one.

To make it clear—this simple workflow will do a PubMed search of any selected text anywhere in OS X, all through your institutional proxy server. Finding an interesting reference while reading an article, highlighting its title, and hitting ^⎇⌘P to get to the PDF always feels like magic.

You can download the workflow here.

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Kako ljudi u Srbiji preživljavaju teror pušača?

Rekao sam sebi da neću biti onaj gastarbajter koji posle godinu-dve van zemlje dođe na odmor, pa se čudi kako u Srbiji uopšte ima struje, tekuće vode, hleba u prodavnici… Ali—kako bilo ko može da ode u kafić, restoran, kafanu, i uz jelo i piće dobije i dobru dozu duvanskog dima? Kako da gledam decu koja sede u poslastičarnici dok im sa stola pored dolazi oblak karcinogena? Šta da kažem njihovoj majci koja puši za tim istim stolom? Zašto posle svakog izlaska u grad moram da vetrim odeću?

Ovo nije pitanje estetike i tolerancije. Gde ima pušača ima i raka:

Isto važi za kardivaskularne bolesti, bolesti pluća, šlog… Kako, onda, prioritet Ministarstva Zdravlja nije potpuna zabrana pušenja? Da li srpski budžet toliko zavisi od poreza na duvan? Ili Filip Moris i ostali toliko dobro lobiraju? Zašto država duvanskim parama ne bi subvencionisala elektronske cigarete?

Ako mi bilo koji pušač kaže da je zabrana pušenja na svim javnim mestima kršenje njegovih ili njenih ljudskih prava, pitam ih da li je i zabrana uriniranja na gradskim trgovima kršenje nečijih prava? Koja je razlika između pušenja i pišanja u javnosti?

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Why doctors shouldn’t use Google services

If you have a Google+ account—and you might not be aware that you do—anyone using Gmail can now email you without knowing your address. You can disable this “feature” in the settings, but having it be opt-out shows yet again how little Google cares about privacy.

Not that there’s anything wrong with that—privacy is a relatively modern invention that younger generations might not care for as much as we do. But you should understand the implications of patients and random strangers being able to leave messages in your personal inbox. Suing P.,,,,,,kmmmmmqmmmdoctors is not a modern invention.

This is why I stopped using all Google services—search included—years ago. The company has become so large, with so many users, that it doesn’t need to cater to fringe interests. And for a business with billions of users, doctors are a fringe group—one that hates change-for-change’s-sake, having to [re-learn an interface][ n. Nnjm interface] “just because”, and not being the true customer1.

Also, the number of people at Google who may access my data is huge. FastMail2, my email provider of choice, has fewer than 10 employees. Gmail alone has hundreds. Not that anyone would be interested in me in particular, but if I ever inadvertently send or receive private patient information through my personal account, I’d rather as few people as possible see it.

Email is fine, but why abandon search? First, I have googled enough ailments and substances, common and obscure, that the add network thought I was an elderly female recovering heroin addict with more than one paraphilia. The adds I would get were in that sense appropriate. Second, because of SEO the only valuable page-one results I would get were Wikipedia entries. Everything else was a hodgepodge of useless Livestrong, Huffington post and five-pages-per-500-word-article-AND-behind-a-login-wall Medscape links. Duckduckgo and, yes, Bing at least help with the first problem while not making the second one any worse.

Google calendar is the only service I would consider using. It is fast, reliable, omnipresent and easy to use. There is, however, that constant nagging fear that they will find some way to integrate it with Google+ and yet again sacrifice functionality to force people into its circle3. This is why I use Apple’s iCloud calendar, its horrendous web interface and all.

Also: Reader. I use FeedWrangler now, but man.

Doctors’ concerns aside, Google is all set to become the network TV4 of the internet—large, bland, and largely not relevant to the people who are. It is already two-thirds of the way there.


  1. This one in particular, as it keeps reminding me that doctors are second-class citizens in the tech world. Electronic health records are made with the billing departments in mind—we are there to provide content. Google services are created to sell adds—we are there to provide eyeballs. 

  2. Yes, it’s an affiliate link. 

  3. crickets 

  4. Or Microsoft. 

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Da li bih sve ponovo?

Da li si zadovoljan Amerikom? Da li bi sve ponovo?

Ovakva pitanja mi često stižu na mejl. Kratki odgovor je—da, apsolutno.

Naravno, odlaskom nisam rešio sva životna pitanja, već sam jedan skup problema zamenio drugim. Ne moram da razmišljam iz koje stranke je šef odeljenja na kome volontiram a iz koje direktor bolnice, i u kakvim su odnosima; da li će me pacijenti gledati popreko jer su lekari po definiciji ili korumpirani ili nesposobni1; da li ću sa 30 godina još uvek biti na grbači roditelja, i kako odgajati sopstvenu decu u Srbiji 2013-te?

Umesto toga, trošim vreme i novac na polaganje milion testova za licenciranje2 i razgovore za subspecijalizaciju3; pacijenti me gledaju popreko jer su lekari po definiciji bezobrazno bogati; slobodnog vremena nemam puno, jer mi prosečan radni dan traje 12 sati a skoro svaki vikend trošim na manijakalno Skajpovanje sa prijateljima i porodicom4. Po onome što sam čuo od prijatelja, pretpostavljam da bih negde u Zapadnoj Evropi u zamenu za slobodnije vikende i blizinu Srbije dobio zatvorenost prema imigrantima i ograničena mogućnost za napredovanje5, za mene još i uz gubitak vremena na učenje još jednog stranog jezika. Sve ima svoje.

Stručni i lični izazovi ostaju: praćenje literature, pregovaranje sa pacijentima, veš mašina koja zbog koje misteriozno iskače osigurač u različitim delovima ciklusa, a savršeno radi kad dođe majstor… Ali, lepo je baviti se tim stvarima bez stalnog straha da će se država urušiti oko vas. Dodatni bonus u Americi je što je većina ljudi ili zadovoljna svojim poslom ili aktivno traži bolji, što je mnogo bolja atmosfera za život i rad od stalnog slušanja jadikovki—često potpuno opravdanih—o teškom životu ljudi oko vas.

A roditelji? Dovedite ih kod sebe gde god da ste, i čim budete mogli. Srbija nije zemlja za starce.


  1. Jer ko je sposoban ume to i da naplati. 

  2. Da, USMLE je samo početak. 

  3. Srećom sam zbog porodične situacije bio ograničen na lokalne programe. Kolege su prosečno trošile $3-4.000 za prijavu, prevoz i smeštaj. 

  4. Ostatak ode na jurcanje za Dorom. 

  5. Ovde sam bez ikakvog prethodnog radnog iskustva završio specijalizaciju iz interne u bolnici u kojoj sam sad glavni specijalizant, a od 1. jula počinjem subspecijalizaciju iz hematologije/onkologije na NCI/NIH. Šta je NCI najbolje se vidi po adresi njihovog sajta: cancer.gov

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The difference between being well and feeling well

Marco Arment discovered an old article in The Atlantic pronouncing the triumph of New-Age medicine. It’s been a while since I’ve read it, but the introduction reminded me of what I thought was its biggest fault in reasoning:

… But now many doctors admit that alternative medicine often seems to do a better job of making patients well, and at a much lower cost, than mainstream care—and they’re trying to learn from it.

Alternative medicine does not make patients well. It makes them feel well. The difference is huge.

Here are two graphs from an excellent free-to-access NEJM article that compared four methods of treating asthma: conventional medicine, placebo, sham acupuncture, and doing nothing1. The first one shows how well the patients in each group felt after 2-4 weeks of treatment.

Ah ha! Conventional medicine was no better than sham (sham!) acupuncture, and both beat placebo inhalers. Alternative medicine wins! Or did conventional medicine lose? At the very least it’s a draw.

Not so fast. The second graphs shows the amount of objective improvement, measured in FEV1—the volume of air you exhale during the first second of breathing out:

If this were the common cold, it wouldn’t have been a big deal. But asthma is not the common cold. People die of it every day, not because they didn’t feel well—though being unable to breathe is doubtlessly uncomfortable—but because their airways were too tight to get any air out of the lungs.

This is why alternative medicine can be dangerous in the wrong hands, with the wrong patient. Improving quality of life is important, but so is curing disease.


  1. Adding real acupuncture to the interventions would have made the study perfect. Some other time, perhaps. 

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Starting the New Year with Slogger

January 1st seemed to be a good day to install Brett Terpstra’s Slogger. Every night, its army of gnomes will go over my tweets, blog posts, completed to-dos, etc. and record them in a Day One journal entry. Not a replacement for a real journal, true, but better than anything I could do on my own.

It’s a Mac-only app that runs from the command line—not user friendly at all. Even so, the installation instructions are straightforward, with some caveats for the not-too-bright, like me:

  • Plugin configuration is done in each individual plugin.rb file, not slogger_config.
  • All config strings (URLs, file paths, usernames…) should be in quotes (“…”), even when in an array (i.e. in square brackets). The Twitter plugin instructions wrongly give an example without quotes.
  • The Instapaper plugin doesn’t work since RSS feeds for folders are no longer supported. I’m still not switching to Pocket.
  • You will need an IFTTT account to log your Facebook posts, using this recipe.
  • Instructions for logging RunKeeper activity are convoluted, but work.

Slogger’s default time for sucking in your data is 11:50pm, when my laptop is usually in sleep mode. The scheduler should still be smart enough to start the app on wake-up. Nevertheless, it’s one more reason for me to get a used Mac Mini. In 2015, perhaps.

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Two podcasts, three doctors, one good show

In the last two months, two of my must-listen podcasts, Systematic and Mac Power User, have had medical professionals on as guests. I don’t usually listen to medical podcasts—Twitter and saved PubMed searches are big enough firehoses—so I thought it would be interesting to hear how my more experienced colleagues use technology. Two of the three episodes were underwhelming, one was stellar.

It started with Brett Terprstra and Dr. Pamela Peeke on Systematic. She has several books targeted towards lay public, and the episode went in the same vein—broad advice on nutrition, well-being, etc. I cringed more than once, but that was to be expected—public health information relies on overplaying the risks and simplifying facts to the point of absurdity1. The one thing I could agree with was how important meditation can be, as mindful meditation might decrease physician burnout. Negative points for not mentioning Mindfulness in Plain English as essential reading, though I haven’t read Dr. Peeke’s own recommendation, The Miracle of Mindfulness.

I had higher hopes for Episode 169 of MPU, since Katie Floyd’s and David Sparks’s guest, Dr. Jeffrey Taekman, has an excellent productivity blog. Alas, McSparky spent more than half of the show being fascinated by the minutiae of what doctors do. Which is better than what followed—long periods of uncomfortable silence while the unprepared guest clicked through every app in his menu bar to see if there is anything worth mentioning2. There wasn’t.

Then another episode of Systematic came on, with Dr. Don Schaffner, a microbiologist3. It was outstanding. Brett was a better interviewer than David, and avoided getting too side-tracked by his guest’s interesting work. But ultimately, the show was good because Dr. Schaffner had useful tips and app recommendations that did not simply regurgitate the latest round of MPU/Mactories/Macdrifter/etc. sponsors. His paper review workflow gave me several ideas I will work on during the holiday downtime. He also suggested a promising contender in my quest to find headphones that will survive more than 8-12 months of intensive use.

One more thing for me to do during the downtime: promote Zotero. Between the developers fumbling Papers 3 and Mendeley being taken over by an evil corporation, Zotero coupled with a few extensions is the best reference manager on any platform. Coming in 2014.


  1. Much like weather forecasts

  2. OK, it was not total silence. You could hear Katie fuming in the background. 

  3. PhD, not MD. Wonder if that explains why the show was better. 

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Ten common residency idioms and phrases

  • I don’t feel comfortable doing that.—I don’t know what you’re asking me to do (nurse to intern); I’m too lazy to do it (intern to resident); I think it’s a stupid idea and there’s no way you can make me do it (resident to attending); You’re not paying me enough to do this crap (attending to administration).
  • It’s a light elective—You don’t need to show up.
  • Needs to read more. (on a written evaluation)—I have no idea how much medicine this person knows. I barely know any myself.
  • The family is reasonable.—Family members don’t ask too many questions and will agree with anything you say.
  • The patient has xyz.—I’ve read in an old discharge summary that the patient has xyz, but have no idea how they established the diagnosis, what stage it is in, or what the hell xyz even is.
  • The head is normocephalic, atraumatic. Pupils are equal, round and reactive to light and accommodation. Sclearae are nonicteric.—If I were to report the physical exam I actually did it would take five nanoseconds, so take these fillers to make it seem like I’ve put in some effort.
  • Thank you for the thorough presentation.—Why did you waste my time with all that useless information?
  • That’s an outpatient work-up.—Administration is already breathing down my neck because of this patient’s length of stay and you’re worried about a mild anemia and a positive hemoccult!?
  • That’s her new baseline.—Her disease is worse and we don’t know why, so I guess she’s stuck with it.
  • Please let me know if you have any more questions.—This is the end of our conversation, so please stop talking. I shall now leave.
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As a one-time interviewer and two-time interviewee…

…to me, this looks flaky. Yes, Scott Adams (of-Dilbert-fame) is right in saying your best bet for success in life is being pretty good in several skills rather than trying to be the best ever in only one. So, a plan like this:

  1. Step one: become a decent entrepreneur
  2. Step two: become a decent MD
  3. Step three: ???
  4. Step four: profit!

might indeed be a good idea. However:

  • Medicine implies altruism. Entrepreneurship implies greed.
  • Programs want their residents to be 100% dedicated to medicine in general and the program in particular. Can you do that with a small business on the side?
  • Physicians in academia, i.e. those who conduct residency interviews, forgo 300k+ salaries so they could dedicate themselves to research and education. Are you sure telling them about your latest money-making scheme is a good idea?
  • As a resident, do you look at each patient as an opportunity to help them and learn from them, or to figure out how to build a business around them?

Residency programs exist to train physicians, not CEOs. Residency slots are already in short supply. Would program directors give a position to someone who is more likely to end up not practicing medicine at all?

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USMLE, ponovo

Dve i po godine od mog prvog teksta o polaganju USMLE-a, malo toga se promenilo. Goljan je i dalje odličan za patologiju (i više od pola Stepa 1), ali se u međuvremenu pojavila i Patoma. Potpuno su eliminisali dvocifreni skor jer je zbunjivao ljude. Zbog sve boljih prosečnih rezultata minimalni prolazni trocifreni će od Januara 2014. biti 192 umesto 1884.

Centralni deo pripreme i dalje bi trebalo da budu fleš kartice. Android tableti i telefoni su sada mnogo dostupniji3. Anki je i dalje prvi izbor, ali ne i jedini. Proces je jednostavan:

  • Pročitajte ovlaš poglavlje iz First Aid-a.
  • Za oblasti za koje je preporučen još neki (opširniji) udžbenik, pročitajte samo one oblasti iz tog udžbenika koji se spominju u First Aid-u2.
  • Pročitajte još jednom sekundarni udžbenik, dopisujući u First Aid stvari koje mislite da treba zapamtiti
  • Pročitajte još jednom First Aid, podvlačeći stvari koje mislite da treba da idu na fleš kartice1.
  • Napravite fleš kartice od svih podvučenih stvari iz First Aid-a, i svih stvari koje ste iz sekundarnog udžbenika ubacili u Frist Aid.

Ako ste sve uradili kako treba, na to poglavlje First Aid-a ne bi trebalo ni da se vraćate. Već ste ga prešli tri puta, a sve što još niste zapamtili je u karticama. Proveravajte se karticama svaki dan, u prevozu, dok čekate u redu, na dosadnim predavanjima. Zato je bitno imati telefon ili tablet.

Dva-tri meseca pred ispit, uplatite USMLE World, i počnite sa tim pitanjima. Kad sam poslednji put gledao, bilo ih je oko 3.000 za Step 1 i 1.800 za Step 2 CK. Mesec dana pred ispit uplatite neki od NBME testova, vidite gde ste i na šta bi trebalo da obratite više pažnje.

Sâm proces prijave za specijalizaciju se nije promenio5. Zbog novih medicinskih fakulteta sve više Amerikanaca bira internu medicinu, ali nema ništa manje FMG-eva. Neki programi će uvek pre izabrati Amerikanca sa lošijim skorovima od nekoga na J1 vizi sa 260 na oba stepa, ali ne svi, čak ne ni većina. Uvek je dobro znati nekoga u bolnici u kojoj se prijavljujete.

Da li uopšte vredi dolaziti ovde, kada ima toliko problema sa primenom ACA? Apsolutno.


  1. To su obično suve činjenie do kojih ne možete brzo doći povezivanjem stvari koje već znate. Ako ste imalo pazili na faksu, to nikako ne bi trebalo da bude ceo First Aid, pošto bi dobar deo tih činjenica trebalo da vam je već ugraviran u pamćenje. 

  2. Najbolji primer za ovo je mikrobiologija i Microbiology Made Ridiculously Simple. Čitajte samo o onim organizmima koji se nalaze i u First Aid-u, što je manje od pola knjige. 

  3. Iako su Apple uređaji bolji izbor za lekare, u Srbiji su i dalje preskupi i nedovoljno podržani. 

  4. Naravno, efektivni minimum za strance je i dalje oko 220 ± 10. 

  5. Ove godine i ja intervjuišem gomilu kandidata. Više o tome čim se završi ceo proces, sredinom marta. 

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