One of the ideas out there in the “3Dprintosphere”, is that seemingly common plastic doo-dads are way too expensive, and would be a lot cheaper if they could be custom fabricated on-site.  A classic example is gel combs – those little plastic things we all use to form wells in our SDS-PAGE gels. For the privilege of owning one of these small pieces of plastic, a reputable manufacturer of such mini-gel apparatus will charge $37 for a pack of 5. Add in shipping costs and you’re looking at $10 a pop, for something that costs maybe 10c to make.

So, SketchUp, Repetier, and PrintrBot to the rescue…

That’s a custom 7-well 1.5mm comb. The reason we did this is to load more sample.  A regular 10-well comb has 10mm deep wells, 5mm wide, so they hold ~75μl each. These wells are 12mm deep and 7mm wide, so they hold 126μl each (previously we had to use tape to join together 2 wells of a 15 well comb to make a wide lane).

This one was printed at 0.15mm layer height using MakerBot PLA filament at 225C with solid rectilinear infill. It took about 10 minutes to design and 16 minutes to print, and uses about 900mm of filament, so assuming a cost of 13c per meter** that’s a 12c material cost. If it breaks or wears out, who cares?  We could print a brand new one every month for 6 years still be ahead on cost. And we can customize the size for whatever sample is needed.

The STL file for this, plus those for standard 10 well and 15 well combs (for the mini-gel box maker known as “big green”), are in this zip folder. I also threw in the Sketchup file with a blank comb-body so you can draw in the lines and use the push/pull tool to design custom well sizes, as we did here for the 7 well version.

Enjoy.

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**PLA density = 1.24kg per liter
A 1kg roll costs ~$45 depending on where you source it
Diameter=1.75mm, radius 0.875mm, pi R squared and all that malarky, so 1 meter = 2.405 cm3
This 2.405cm3 weighs 2.982 grams.
So a 1kg spool has 335 meters, i.e. 13.4c per meter

One of the latest things we have in the lab’ is a 3D printer – a PrintrBot Simple Metal. I bought it over the summer and assembled it from a kit, which took about 5 hours. There are lots of things available to download and print from Thingiverse, or the NIH 3D print exchange, but if you want to make things from scratch, you need to learn to design in 3D using a program such as Sketchup. It’s free to download but there’s a steep learning curve and this was a big obstacle for me.  Now I’m over that initial hump however, we can make things for the lab…

3D printed door-handle extension

The lab’ door opens outward, so opening it from the inside is easy when you’re laden with stuff or just wearing gloves – simply push and your elbow.  BUT, if you’re outside and want to get in, you can’t pull the door handle with your elbow.  So, I designed an extension to bolt onto the handle, providing a hook so you can pull the door open with your forearm, without touching anything with your hands.  Here’s the finished article…

The .STL file is available here (in a zip folder because web host will not allow direct hosting of STL files) if you want to print your own. The screws used were standard 3/4″ steel sheet metal screws, the kind used for air duct work and available in packs of 100 at Home Depot.  There’s a tab on the lower piece which grips against the ell in the metal handle, preventing it from spinning around. This one is for right handed opening doors, but in the next few days we plan to make one for left-handed doors too, and will update the STL then. The STL also contains some support material that has to be cut away after printing.

Trough for multi-pipeting small amounts

We use a Seahorse XF96 in the lab’. Each well has 4 drug-loading ports, but they only hold about 25 ul each. If you’re loading small amounts of expensive mitochondrial inhibitors (rotenone, FCCP etc.) the troughs typically available from lab-ware suppliers are just too big – twice as long as necessary and way too deep…

Our 3D printed version is a lot smaller, holding about 2ml instead of the usual 20-30 ml. Below is a picture, and the STL file is available here.

We’ve also played around with a few small dishes and chambers for patch clamping, various tube racks and holders, and some accessories for the PrintrBot itself. One issue we’ve come across is the water-tightness of flat printed surfaces – even with solid infill we seem to always end up with some leaks (hence the trough above was designed with angled walls that provide a much tighter seal).  Also we’re not sure yet about the long-term durability of PLA in a lab setting.  It’s a biodegradable corn plastic (polylactic acid), so might not hold up well to autoclaving etc. (we already had a tube rack deform when someone accidentally left the water bath cranked up to 70C).

We’ll be posting more STL models as they come.

Well, new to us at least.

Over the past couple of months, we’ve been lucky enough to absorb an adjacent lab’. Up to now, our main lab’ was 7420, at the bottom center on the plan shown below, with a small cell culture room in the back (20A). We also used the lab’ next door (7424) on the same corridor, but this was problematic because there’s no connecting door. For security reasons the adjacent lab had to be locked when unoccupied, so to get there meant removing gloves and fiddling with keys while carrying an ice bucket. Another problem – we were using the back room (20A) for animal work, but because it’s a dedicated cell culture room, it has positive air pressure. So, all the dander and allergens and other gunk would float out into the main lab. Not good when you’re allergic to mice!

The cost to open a doorway between the 2 big labs was prohibitive, but for a while we’d been aware there was an old connecting door to the lab behind us (7512 on the plan). That room was used by Alan Smrcka ‘s group as a student office and general storage room, and the door was simply blocked on both sides with drywall and a few wooden shelves/cabinets. The lab’ once belonged to a former Dept. chair, but was never officially decommissioned when he retired a few years ago, so the cupboards were full of old supplies, chemicals and defunct equipment. So, we approached Alan and he very generously agreed to a swap – room 7512 in exchange for 7424. After a few weeks of construction dust, we now have a new lab, and finally 3 rooms of contiguous space. It wasn’t quite like this but you get the idea…

The new space is nothing short of a revelation for the way we work. We now have a simple arrangement with in-vivo stuff in the new room (7512), cell stuff in the middle, and biochemistry in the main lab at the front. The great thing is there’s a fume hood in the new room, so we can keep allergen exposures to a minimum elsewhere in the lab. Also now the cell culture room (20A) with positive air pressure can finally serve its intended purpose.

Here’s what’s left of the connecting door, looking through from the new lab’ into the cell culture room. On the right is our cardiomyocyte preparation rig, making it easy to transfer the freshly prepared cells into the cell culture hood and incubator. There’s still some finish work to be done on the floor and the bench-edges.

This is now our perfusion bench. On the left is the surgical area with dissecting scope, ventilator, EKG, thermal pad etc.  Then on the right are two separate Langendorff heart perfusion rigs. There’s a third rig out of view, on the opposite side of the new lab. Due to fire regulations we’re not allowed to use the top shelves near the ceiling for storage, so those are blocked off.

We also relocated our HPLC to the new lab. Here it is next to the fume hood…

In the cell culture room we now have our 2 seahorses – XF24 and XF96.  This used to be the bench where all our perfusion gear was. You can also see the gas perfusion system mounted on the shelf – we do some fun things involving flooding the plates inside the seahorse with argon gas, as reported here.

Here’s another view of the cell culture room showing the hood, with the seahorse bench on the left…

During the reshuffle we were able to divest some old equipment that was broken no longer being used.  A key piece was our Aviv Model 14 spectrophotometer, which Jack Aviv himself came to collect. It had served us well, and was the source of several publications, but had sat unused for many years and took up a lot of space. Here it is in the back of Jack’s van…

The other thing this move allowed us to do, was consolidate our refrigeration in the front lab’, so now we have 4C, -20C and -80C all in one place.

Most of the demo’ work was done by UR facilities, plus moving electrical panels, putting in new floor tiles to bridge the gap, some HVAC work to balance out the flows, removal of old telephone lines, replacing all the fluorescent light tubes etc. Some things we did ourselves – for example we used the opportunity to do some paint touch-up throughout the lab (the drywall was pretty beaten up in places). Here’s our technician Bill hard at work – this is how we roll!

Environmental Health Sciences also helped us to dispose of the various chemicals through the hazardous waste program. We managed to fill 3 dumpsters with old equipment and supplies from the cupboards of the 7512 lab – a bonus for the Department is the lab is now clean and no longer a hazard liability.

Like all moves this one was pretty disruptive, but the new space really works well. The 3 Langendorff rigs are already cranking out data. Having all the cell culture stuff in one room means less contamination. No more messing with gloves and keys to get between labs.  The new lab has a door leading out to the elevator lobby, which gives us another fire escape route, plus that’s where the bathrooms are located so it’s easier to go answer the call of nature during experiments!  All in all a very worthwhile process.

A while ago I documented some data problems in a JBC paper, including a failed attempt by the authors to correct the paper, followed ultimately by its retraction.

Well, guess what showed up at Frontiers this week… the exact same paper. The title is almost the same, huge blocks of the text are the same, and the majority of the data and figures (minus the mistakes during figure preparation) are the same. Without making any comments on the reliability of the data in the new paper, which I haven’t examined in detail yet, the following questions come to mind….

• Did the editors at Frontiers know the paper had been retracted from another journal?  If so (or not), how would this have influenced the peer review process?
• The authors listed on the retracted paper and the new one are identical. I don’t know how other people run their labs, but if my lab had a paper retracted for questionable data integrity, the person responsible for those problems would be out the door faster than you can say “Committee on Publication Ethics”. Keeping the same authors suggests that either Dr. Donmez is an extremely forgiving employer and chose not to fire the subordinate responsible for this mess, or that she was personally responsible for the problem data so there is no subordinate to fire.**
• What about copyright? The original version of the paper is still up at the JBC site for all the world to see. Does Frontiers have the right to publish the same information, in clear in breach of JBC’s copyright?  How does copyright work on a retracted paper?
• How should episodes such as this inform how we deal with retracted papers in the future?

Regarding the last point, perhaps a good starting point would be a check-box on the intake form for journals, stating whether the work is a republication of a previously retracted work. Perhaps such papers could then be accompanied by a statement with assurances that the original data have been scrutinized to ensure their integrity.

** I’ve run into this problem before – seeing a paper in the review stages with creative data presentation, and then seeing it appear elsewhere with the exact same list of authors. How many more papers are out there, where authors dodged a bullet in the review stages but made it to press somewhere else?

UPDATE (4pm 9/2/2014) – I just learned via PubPeer that a paper from Rui Curi (favorite South American dood who threatened to sue me) was re-published in an open access journal OmicsOnline, which is on Beall’s list of predatory (pay-4-glam) journals. Incidentally, the original paper was in J Lipid Res, also an ASBMB journal (like JBC), and so the original full-text is still up there on the JLR website. Again, the copyright question arises – does omicsonline own the paper now?  Has anyone done an analysis to see how much of the content of these new predatory open access journals is comprised of stuff retracted from other places?

UPDATE 2 (9am 9/3/2014) – Following an email last night, I have now heard back from the Frontiers in Aging Neuroscience EiC, Gemma Casadesus Smith. They were “unaware of this issue and will look closely into it”.  Hopefully that’s not a euphemism for try to forget about it until all washes over, as frequently seems to happen at other journals.  Now we play the waiting game…

About 6 months ago I wrote this post, about the trouble I was having in getting 3 problem papers by a single author dealt with by journals. The author in question was Gizem Donmez of Tufts University, who in 2013 threatened to sue me for defamation based on the things I had written about her science. The papers were:

J. Biol. Chem. 2012;287;32307-32311; PMID22898818 – Retracted July 2013
Cell 2010;142;320-332; PMID20655472 – Retracted this week
J. Neurosci. 2012;32;124-32; PMID22219275 – Still intact

As you can see from the 2nd entry there, the Cell paper has now been retracted. While this is indeed good news, it is by no means indicative that all is well in the world.  In-fact, the story of how this played out indicates deep problems at Cell. Here’s the time-line…

August 2012 – Original email by me to Cell using a pseudonym. The anonymous contact who sent me details of these papers to blog about also indicated they had contacted the journal. No responses were received despite multiple emails. Attempts to contact Dr. Donmez’s Institutional Research Integrity Officer and Department Chair were also ignored.

September 2012 – Papers were blogged about on my now defunct site-that-must-not-be-named. Numerous emails with links to the blog post were sent to all interested parties, including the Ellison Medical Foundation which had just awarded Dr. Donmez a prestigious “New Scholar in Aging” award, largely on the basis of work published in these papers. To date, Ellison has refused to engage in any conversation regarding the integrity of data used in her award application. The ORI was also informed, and to the best of my knowledge their investigation is ongoing.

September 2013 – I contacted Cell again using my real name, reiterating my concerns. Cell responded 2 months later, saying this.. “Despite some apparent superficial similarities, upon extensive examination we were unable to find any compelling evidence for manipulation or duplication in those panels and therefore are not taking any further action at this time.” The email came from Sri Devi Narasimhan, an editor at Cell who trained with Heidi Tissenbaum at UMass, who in-turn trained in the lab’ of the paper’s senior author (who also happens to be on Cell‘s editorial board).

January 2014 – I complained to Cell about this rather obvious appearance of conflict-of-interest, and blogged about it here. Over the course of the next month, several attempts were made to contact Cell, including numerous promises from Editor-in-Chief Emilie Marcus’ assistant that she would get back to me. That never happened. To date I have received no communication whatsoever from Dr. Marcus regarding these issues.

February 2014 – I decided to involve the Committee on Publication Ethics, COPE. There ensued many emails to establish correct procedures for raising a formal complaint (TL/DR – one must ensure all avenues at the journal have been exhausted before COPE will take on a case. This is easy – when a journal’s EiC goes incommunicado, all avenues are exhausted). The full text of my complaint about Cell is here, (minus all the attachments) but it really boils down to the following…

In refusing to initially respond to an anonymous correspondent, and then further refusing to respond to emails and follow up requests for more information using my real identity, the journal breached Code Section 15.1 “Editors should respond promptly to complaints and should ensure there is a way for dissatisfied complainants to take complaints further”.
In assigning a misconduct investigation to a staff member who is a trainee of a trainee of the lead author of the paper in question, the journal breached Code Sections 2.1 “Duties include informing readers about steps taken to ensure that submissions from members of the journal’s staff or editorial board receive an objective and unbiased evaluation” and 17.1 “Editors should have systems for managing their own conflicts of interest as well as those of their staff, authors, reviewers and editorial board members”.

March to July 2014 – I made numerous attempts over the past few months to find out what’s going on at COPE and at Cell. While I don’t wish to reproduce all the emails at least 26 of them over the course of 6 months), the gist of the conversation is as follows:

Me: What’s going on?
COPE: We contacted the publisher
Me: Why the publisher? It’s the editor I’m complaining about.
COPE: Although the editors looked into your case, the publishers had not yet completed an investigation. Elsevier told us they’re still looking into it. We’ve been pushing hard on this for the past few weeks.
COPE: The editors are now investigating the 2nd round of concerns you raised in your blog post.
Me: So let me get this straight. There are actually 4 investigations – one each for the editors and the publishers, and one for each round of allegations. So far after 2 years, only 1 of these 4 is complete and the outcome was “unable to find any compelling evidence”.?
COPE: Yes. We’ll keep you posted.

August 2014 – Someone (not me) recently revived the PubPeer thread on this paper, independently “rediscovering” the various image problems within it.

August 12 (yesterday) – Finally, the paper has been retracted, with a rather detailed retraction notice indicating a LOT of image problems. I want to compare and contrast the statement from the Cell editor further up the page with the retraction notice…

Cell editor Jan’ 14. “Despite some apparent superficial similarities, upon extensive examination we were unable to find any compelling evidence for manipulation or duplication”.

Cell editors Aug’ 14. “It has come to our attention that several figures in the paper contain images in which gel lanes were spliced together without appropriate indication. There are also instances of image duplication”.

Given the first statement, you really have to ask if the Cell editorial team is living in an alternate universe, where the term “extensive” means half-assed? It’s also somewhat troubling that there’s been no formal contact from the journal to the person who actually raised the complaints. Although there’s no precedent or requirement for such, you’d think as a matter of courtesy that a journal would formally notify a correspondent of an impending retraction, rather than just have them learn about it via social media. But, we already know basic manners aren’t a strong suit at Cell, so no big surprise there.

What next?
At this point, I have not been contacted at all by COPE, so I’m assuming their investigation into potential breach of code-of-conduct at Cell is still ongoing. Given that Cell and Elsevier are two of COPE’s biggest customers/subscribers, I can imagine there’s rather a lot of pressure on COPE to make this story go away. Let’s hope that doesn’t happen – Cell screwed up really badly here and if heads don’t roll then this case becomes yet another indicator of how corrupt the academic publication system really is.