Upgrading the Open Access Button

The Open Access Button is getting an upgrade.

Back in January, I talked about extending the Open Access Button to capture links to open access journal papers.

That patch is going to go live real soon now.  There’s some minor tests I need to close off prior to launch but we’re closing in on that.  You can see the on the OAButton github repository.

Once this patch is live, we’re going to start collecting links for Open Access versions of publications and start sharing those with people.

This works pretty simply – the first time a pay wall is hit for a paper, we will now try to determine the author email address and then notify the author that the research is unavailable to the public.

We provide a link that the author can click on to submit an open version of their paper.

Every time someone hits the pay wall after that, the user will be notified where to find the open version of their paper.

We still need your help on this.

There are still some rough edges here.  Right now, I only allow the author to submit the link.  That means we have no way for the general public to participate in supplying links to open versions of papers.  I’m doing this because I don’t know of a good way to prevent abuse where invalid links are submitted.

If we can solve that problem – we can provide a public API where individuals can start contributing links to open access papers.  Cracking this nut would be a huge win.  If we could provide a public API – we can build more tools to integrate to the OAButton and we could dramatically increase the number of people contributing links to papers.

We could also use some love to restyle some of the HTML emails and some of the webpages.  If you have design skills – we need you too. :)

This stuff is important.   Let’s fix this.

A note about self deposit repositories:

I didn’t re-use any of the self-deposit systems that individuals and libraries have setup for themselves.  Unfortunately – there’s no rational way of integrating any of these things.   While authors may have deposited a copy of a  pre-print of final draft somewhere, I have no way of determining where that is.  Even if I did, I have no way of querying that system.  I have no way of resolving if the document I find in the system is the same as the document that has been blocked.

If you run one of these systems – we want to work with you.  We just don’t have a way to do that yet.  Let’s figure this out.

Campbell Walsh Urology 11th Edition will revise PVPS risks to 1-2% of patients

I win at the internet.  Sort’ve.

Post-vasectomy pain syndrome has had this “1 in 1000″ patient number floating around for a while, and I’ve never been able to track down where it came from until the last couple of months.   Turns out – that numbers is bunk.

After a series of 35 emails back and forth with Elsevier, the publisher of Campbell Walsh Urology – I can confirm now that the 11th edition will include dramatically higher risks for incurring post-vasectomy pain syndrome.

The 10th edition has this to say on the topic:

Up to 30% of men have short-term scrotal pain lasting a few weeks. However, postvasectomy pain syndrome, or long- term scrotal pain after vasectomy, occurs in approximately one in 1000 vasectomies, although some report the incidence to be as high as 15% (McConaghy et al, 1996; Awsare et al, 2005; Tandon and Sabanegh, 2008).

If you take the time to go through those citations, no such claim is actually made.

McConaghy 1996:

Following a study by McMahon et al. which found that 33% of patients were troubled with chronic testicular discomfort following vasectomy [1], a study was undertaken at our hospital to examine ways of reducing the incidence of this problem. This work has been published recently [2] and we would like to draw your readers’ attention to the relevant findings.

This may result from congestive epididymitis or the development of sperm granuloma. The incidence of chronic orchalgia is quite high (12–52%). [5] The proportion of patients, however, whose quality of life was affected, or those who sought treatment was much lower (2.2–15%)

Tandon 2008 is more complex.  It has this to say:
PVPS is disappointingly common and difficult to treat. Although early pain lasting for a few weeks is fairly common after vasectomy (present in up to 30% of men), longterm pain requiring some kind of intervention or surgical therapy occurs in up to one in 1000 vasectomized men [4].
Tracking down the claim for one in 1000 vasectomized men in citation 4 gives us :
Sandlow JI, Winfield HN, Goldstein M. Surgery of the scrotum and seminal vesicles. In Wein AJ, Kavoussi LR, Novick AC, Partin AW eds, Campbell-Walsh Urology, 9th edn. Philadelphia: WB Saunders, 2006: 1103–9

So what we have is Campbell Walsh citing a paper which cites Campbell Walsh.

There’s never been any evidence that supported the claim of 1 in 1000 number.

So that’s the good news.  That number is going away.

I’m told by the reviewers in Elsevier that they will be using Leslie 2007 for most of their new data and they will also be using the AUA guidelines.

Unfortunately, you won’t be able to verify this until 2016 because Elsevier can’t seem to figure out how to use the internet to publish errata.

Yes – you will need to wait for the dead tree version of the book to come out.

The irony here is a bit thick even for me.

BJU offers open access to Leslie 2007.  After I compiled the trail of papers that made this error possible – I asked to review the draft of the new chapter on vasectomy.  That was October 1.

Here’s the response:  “..it would be highly inappropriate to provide a draft chapter prior to the text being published.

Screw you Elsevier.

You can call me The Doctor

tl;dr – I’ve killed the 0.1-0.25% occurrence rate line in UpToDate. Your doctor can verify the change in the section “Vasectomy and other vasal occlusion techniques for male contraception”. The newly revised number is simply : 2% for severe life quality affecting pain. Your doctor may not be aware of this as the change is not listed yet in the changelog that UpToDate provides users.

Edit: UpToDate has no intention of making this more visible.

No, it is not an oversight that the change is not in What’s new. Only selected topic updates will appear there, and generally those that represent significant alterations in treatment-related decisions.


So I had my surgery on of all day’s – Valentine’s day.

As they wheeled me into the operating room, I told one of the nurses that I was hoping an entirely different kind of valentine’s day. In a southern drawl, she said:

You just tell the boys back home that you were naked with three cute brunettes.

So, it’s been 3 weeks post-op and I’m happy to say that it looks like surgery was successful.   There’s still another 3 or 4 more months to go to be completely sure, but right now – things look really really awesome.

That would be enough for me to do the happy dance, but the thing that’s had me grinning from ear to ear since Friday?

I got my edit to UpToDate accepted.  It’s a small tiny edit, but it’s one that fixes an error that’s been perpetuated for about 30 years near as I can tell.

For those that are unaware, UpToDate is a massively deployed clinician’s database used by doctors around the world as a decision support resource. It’s used by 700,000 doctors globally. That’s a lot.  When I first started posting up on Reddit a couple months back, a redditor pointed me at the numbers in UpToDate as a reference that all doctors are going to use as a point of reference.

Before March 1, 2013, you would have found this in UpToDate:

The post-vasectomy pain syndrome is distinct from post-procedure pain, however, there is some controversy regarding its definition, and therefore prevalence. Rates for the post-vasectomy pain syndrome have been reported as 0.1 to 0.25 percent [41,42]. However, surveys have found that “troublesome” post-vasectomy pain is reported by as many as 15 percent of men, with pain severe enough to impact quality of life in 2 percent; survey respondents, however, may not have been representative of all post-vasectomy men [43,44].

That bold section is gone now.  Without it, it reads quite differently.  It looks like this now:

Historically, rates for the post-vasectomy pain syndrome have been reported as very low (<1 percent). However, surveys have found that the incidence of “troublesome” post-vasectomy pain is reported by about 15 percent of men, with pain severe enough to impact quality of life in 2 percent; survey respondents, however, may not have been representative of all post-vasectomy men [40,41].

I’m annoyed still that the <1% number shows up at all.  The two works cited by UpToDate in the newly revised text only show data that support the 15% occurrence rate.  You can read it yourself in Manikandan 2004 and McMahon 1992.

UpToDate has this to say on the matter:

Incidence reporting in the literature varies widely, The lower incidence figures reflect older literature, with the more contemporary data suggesting that the incidence of this problem is probably higher.

(emphasis is mine)

This weirdly reminds me of watching traders dissect the wording of the Fed every time a rate announcement is made in an attempt to find the ‘true’ meaning of the wording. I think my chinese ancestors called this “reading tea leaves”.  But I digress.

The snarky part of me wishes they’d reword the first sentence to “Historically – we couldn’t bother to do division properly, or read anything.”.  Just before I left for Winter Haven, I ended up pulling the articles cited in UpToDate.  What I found was pretty bad. You can see the full details here.

It turns out – the M in MD is not for math.  Of the two citations, one was a completely different topic, and the JAMA study from 1984 never made any claim that supported the 0.1 to 0.25% occurrence rate.  In fact, the study in 1984 explicitly shows 187 patients out of 10,590 had chronic pain.

I guess calculating 187/10,590 is a really hard thing to do.

The literature does vary widely, but as far as I can tell – there’s still no evidence to support the historical figures.   We can argue about the strength and validity of particular studies, but you don’t get to argue about numbers that just aren’t there.

As they say:  Every man is entitled to his own opinion, but not his own facts.

This kind of mistake happens all the time.  If you haven’t been following the mess going on in cancer research or the debacle that’s going on in academia with respect to peer review – it’s a disaster.   Statistical errors happen all the time now – it’s estimated that it’s happening ~15% of the time.

That though is a rant for another day.  Today – I’m celebrating my small victory.

On a side note – every email I ever got from UpToDate was addressed to “Dr. Ng”.  If anyone else wants to call me “The Doctor” – I’m totally cool with that.

Next post – something entirely nerdy.

Cutting and pasting from German is hard

Sometimes people mess up translations.

Maybe it’s the gutteral sounds of German.

Medline incorrectly got the lower bound of chronic pain post vasectomy as 0.5% when it should be 3%.  Here’s the correction I’ve filed with Pubmed and the original full text (in German).

PubMed link: http://www.ncbi.nlm.nih.gov/pubmed/21845426

You can find the data in Table 2.

PMID:  21845426
TITLE: Ischemic testicular necrosis following vasectomy: rare and typical complications of an outpatient procedure
PUBLISHER: Urologe A
TEXT: Late complications are chronic pain (0.5-18%), pain during sex (2.9%), hydrocele (0-4%) as well as spermatocele (1.6%)
CORRECTION: Late complications are chronic pain (3-18%), pain during sex (2.9-5%), hydrocele (0-4%) as well as spermatocele (1.6%)
NOTE:  The data in question is in Table 2 on the fourth page. I’ve attached the article for your reference.

Original journal article:  Ischemic testicular necrosis following vasectomy: rare and typical complications of an outpatient procedure