On my recent submission of a manuscript to the Journal of Memory and Language (an Elsevier journal), I was faced with the unexpected task of having to provide  “Research highlights” of the submitted manuscript.  Elsevier describe these highlights here, including the following instructions:

  • Include 3 to 5 highlights.
  • Max. 85 characters per highlight including spaces…
  • Only the core results of the paper should be covered.

They mention that these highlights will “be displayed in online search result lists, the contents list and in the online article, but will not (yet) appear in the article PDF file or print”, but having never previously encountered them, I was (and am still) a little unsure about how exactly they would be used (Would they be indexed on Google Scholar? Would they be used instead of the abstract in RSS feeds of the journal table of contents?)  The thought that kept coming to me as I rephrased and reworked my  highlights was “they already have an abstract, why do they need an abstract of my abstract?”

Having pruned my five highlights to fit the criteria, I submitted them and thought nothing more of them. .. until tonight.  I checked the JML website to see if my article had made it to the ‘ Articles In Press’ section and rather than seeing my own article, saw this:

This was my first encounter of Research Highlights in action.  I was impressed.  I’m not too interested in language processing, so would never normally have clicked on the article title to read the abstract, but I didn’t need to. The highlights were quick to read and gave me a flavour of the research without giving me too much to sift though.  I guess that’s the point, and it’ll be interesting to see whether that  is maintained when every article on the page is accompanied by highlights.

It’s hard to tell if the implementation of research highlights in all journals would improve the academic user-experience.  No doubt, other journal publishers are waiting to see how Elsevier’s brain-child is received by researchers.  But there is another potential consequence that could be extremely important.  In the example above, I was able to read something comprehensible to me on a field a know next-to-nothing about.  In the same vein, maybe these highlights will be the first port of call of popular science writers looking to make academic research accessible to laymen.  If the end-result of the research highlight experiment is that a system is implemented that helps reduce the misrepresentation of science in the popular media, then I would consider that a huge success.

A recent submission to the Journal of Memory and Language, an Elsevier journal has made my hyper-aware of how the way a manuscript’s progress through the Elsevier Editorial System (EES) is indicated.  For future reference, I’ve summarised the story-so-far for a recently revised and resubmitted manuscript.  (The worst thing for a compulsive checker like me is that you’re not e-mailed about changes in status, you have to login to the EES and check to see whether the ‘Status Date’ or the ‘Current Status’ has changed.  Every few weeks you get that variable-ratio reinforcement that just reinforces your maladaptive checking behaviour!)

I’m not sure if the ‘Current Status’ stages I list below are universal for all Elsevier journals, or even for all manuscripts within the the Journal of Memory and Language, but here’s what I’ve been through so far.  (Elsevier have a few more details on some of these statuses here: http://support.elsevier.com/app/answers/detail/a_id/160/~/paper-lifecycle-from-submission-to-publication)

Submission

  • “Submission Being Processed” – 16/11/2010: The manuscript is submitted and an e-mail is sent to the corresponding author with EES login details.  The manuscript is assigned to an editor by the journal office staff.
  • “With Editor” – 18/11/2010 (estimated): Presumably an editor makes sure the thing is worthy of being sent out for review and identifies appropriate reviewers.
  • “Under Review” – 24/11/2010: The peer review process starts.
  • “Required Reviews Completed” – 24/12/2010: The manuscript is sent back for an editorial decision.
  • “Revise” – 1/1/2011: E-mail sent to the corresponding author indicating the editorial decision.

Revision 1

  • “Revisions Being Processed” – 20/1/2011: The manuscript is resubmitted and another e-mail is sent to the corresponding author
  • “With Editor” – 20/1/2011: Presumably the editor makes sure the thing is worthy of being sent out for review again…
  • “Accept” – 5/2/2011: or accepts the revised manuscript without a second peer-review.
  • Completed” – 8/2/2011: I don’t know what this stage means.  Maybe it’s an acknowledgement of my receipt of the decision letter.  Incidentally, there are now two additional visible columns: “Date Final Disposition Set” (Feb 08, 2011); and “Final Disposition” (Accept).

Publication

At this point the submission gets closed on the Elsevier Editorial System and gets moved onto an author tracking system (http://authors.elsevier.com).  One of the most important developments is the assignment of a DOI – it’s doesn’t go live until the proofs have been created, but it ‘s assigned and can be used to link to the article in the future. From now onwards, e-mail notifications seem to arrive with every change in status.

  • Expected despatch of proofs notification – 10/02/2011: A date for receipt of manuscript proofs (the journal-formatted pdf) is assigned.
  • Return of “Journal Publishing Agreement”, “Funding Body Agreement” and “Order Offprints” forms requested – 10/2/2011: A link to these forms is e-mailed and they can be completed and submitted online.  This makes a great change from the procedure of having to get snail-mail signatures from all authors, which is a real pain if collaborating with people at multiple institutions.  Once submitted, the status comment changes to…
  • Status comment changed to Publication date not yet known – 10/2/2011
  • Uncorrected Proofs made available and return with corrections requested within 48 hours – 18/2/2011 (Consistent with the tracking system information): This was done through the elsevier.sps.co.in/authorproofs/ website.
  • Status comment changed to No further corrections can now be made – 19/02/2011: ‘Proofs returned’ row also added, with the same 19/02/2011 date.  DOI link still dead and manuscript is still not yet available on the ‘Articles in Press’ section of the JML section of the ScienceDirect website.
  • PDF made available as an ‘Articles in Press’  – 02/03/2011: But the DOI link still doesn’t work.
  • DOI link made functional – 08/03/2011.
  • Article published in print journal – 05/2011.

Having just skimmed the Lifehacker article below, I started thinking about what habits I have started incorporating into my work-day, and what habits I really need to cultivate.

Lifehacker’s “Why and How I Switched to a Standing Desk”

Drinking More Water: At the start of the year I bought a Brita filter jug with the aim of drinking more water.  Seeing the jug on my desk every morning compels me to fill it up and I probably drink a couple of litres throughout an average working day.  This new habit has got rid of a lot of evening headaches and I’m pretty happy with it.  More frequent toilet breaks don’t hurt with breaking up the monotony of a day sat at the desk either.

Standing Desk: There seem to be a few benefits to making the switch to a standing desk.  First, my posture is worsening by the year, and I seem to be collecting muscular pains which are exacerbated by hefting an all-action two-year old around in my spare time.  I imagine a standing desk would get me focused much more on my posture and the body-mechanics that facilitate my working day.  Second, anything to get a bit more physical activity into my life right now would be a good thing – Scottish winters aren’t blessed with an abundance daylight hours or days that scream “Go out for a run” at me.  The barrier making the conversion seems mostly to be social. I don’t want to become ‘The guy in Psychology who has his desk up on reams of printer paper.’  I’m also worried that I wouldn’t make it through the initial 5-day breaking-in phase.

Running: I ran my first half- and full-marathons in St. Louis.  As part of the training for these events, I got into a nice routine of running around Forest Park (close to 7 miles) at least twice a week.  that’s fallen by the wayside recently.  I hope it’ll pick up again in the summer, but I think I’ll try and catalyse that change by going for runs during my lunch break.  I just need to find a suitable shower facility in order to maintain basic standards of hygiene.

Being less wasteful with toner/paper: I don’t like reading journal articles on computer monitors.  Therefore, I print thousands of pages a year, most of which I only read once.  Most of these articles end up catalogued in my Endnote database (if they’re lucky) and locked in a metal filing cabinet with a few notes scrawled on them.  That’s quite a waste of paper and ridiculously expensive toner, which I now have to buy myself.  Motivated by saving trees and money, I’m starting to consider other options.  Now that they’ll display pdfs, I’ve thought about a Kindle; the e-ink is easier on the eye than an LCD screen, the battery lasts for weeks and they’re (relatively) cheap.  BUT they won’t display colour, something I need if I’m to follow the neuroimaging papers I read.  Colour alternatives like the iPad and Nook Colo(u)r have some combination of a shocking battery life, back-lit screens and a horrendous price-tag and I’m not sure it’s worth taking a punt on a gadget that may end up presenting me with more problems than it solves.  For instance, I don’t know how I’d make notes effectively on an electronic pdf document using each of these devices.  I’m settling on the thought that I’ll wait for colour e-ink before committing to wasting less paper, but it does seem like a shame that there isn’t something suitable on the market right now… and I’ll probably be waiting years.

I’d be interested in reading comments from anyone who has converted to a standing desk or bought a Kindle/iPad for the purposes of reading journal articles.  Nothing’s ever going to be without its own problems, but do these innovations improve overall working conditions?

University of Leeds, Parkinson Building with t...
Image via Wikipedia

Last week, for the first time in just under than three years, I visited the Institute of Psychological Sciences at the University of Leeds.  On Thursday attended the Greater Yorkshire Memory Meeting and the next day, with Clare Rathbone of Reading, gave a seminar on some research and our experiences of postdoctoral study.

It was great to see some old faces and great to be back in a city I know well.  The trip was also timely, giving me the opportunity of a long train journey down on which to read plenty of journal articles and devote some time to thinking about research.  But what I got most from the trip was a tremendous appreciation of the  enthusiasm, intelligence and endeavour of the PhD students I encountered.  It was quite wonderful to speak with them about their research and to get a sense of the plasticity of their approaches to science.  They aren’t yet ‘world-expert researchers of X’ or ‘wed to theory Y’ , but are revelling in the acquisition of expertise… it’s a very exciting time of their careers and as a result they are invigorating people to speak to.

It got me thinking about the formation of my own lab.  Whilst the UK system doesn’t generally allow for the self-contained modular lab that I so enjoyed being a part of in the US, working with people you look forward to encountering and speaking to on a daily basis would undoubtedly inoculate you against some of the increasingly prevalent sadnesses of the British University system (which has already started encroaching on the student experience despite assertions from the coalition government that it wouldn’t, e.g. through the cancellation of student assessment due to paper shortages).  I look forward to taking on PhD students with as much enthusiasm as those I encountered in Leeds – I just hope that those who are good enough to make a difference to society through research aren’t forced away from a postgraduate career by the “fair and affordable” system that will see them in up to £27,000 of debt from tuition fees alone before they even contemplate another three years of study.

In the past few weeks, a couple of students have approached me asking if I would be willing to take them on as a summer intern.  I scrabbled around to gather some information on the sort of scheme that these students were after.

Here are my summer internship pass-notes:

  • Typically they offer £180-£200 per week to the student to engage in a research 6-10 week project during their summer holidays.
  • Whilst students should liaise with their proposed PI during the application process, they are generally expected to write the application.
  • Students considering internships should be interested in pursuing research as a career after the completion of their degree and should be on course for a solid 2i or 1st class degree.
  • Closing dates tend for the various schemes tend to be towards the end of February/March.

Here are some links to schemes I am aware of that would be particularly suitable for me as PI, along with some points specific to each:

The BPS Undergraduate Research Assistantship Scheme: £200 per week, for a 6-8 week project.  PI must be a member of the BPS. Student must be in the punultimate year of their degree.
Wellcome Trust Biomedical Vacation Scholarship: £180 per week for 8 week project.  Student must be in a middle year of their degree.
St Andrews Undergraduate Research Internship Programme: PI must be a researcher at the University of St Andrews.
Nuffield Undergraduate Research Bursary in Science: £180 per week for 6-8 week project.  Student must be in a middle year of their degree.
UPDATE 28/12/2010: Here another scheme from Medical Research Scotland:
Medical Research Scotland Vacation Scholarship: £180 per week plus £50 per week for the sponsoring lab.  Placements must be in Scottish universities.  Applications must be made by potential supervisors, not students.

It’s been a while.

Settling in to a new job has been terrifying and tiring in equal measure.  The seemingly boundless spending of the early weeks has been replaced by an awfully adult awareness that the only thing you can’t buy is time: more time in my day to prepare for contact with students, to write grant applications, to read journal articles, to blog (yes, this is something I feel I ‘should’ be doing)  but most of all, to think.

Whilst I find it very easy to develop my thoughts on how the Comprehensive Spending Review affected me (not much, yet), whether I support the student protest movement against tuition fees (I do, wholeheartedly), and why QPR saw fit to lose on national television in the only fixture I’ve seen them play this season (regression to the mean), I’m struggling to come up with original ideas for experiments that will be an instant imaging hit.  I’m in the profession of thinking, so it’s certainly no good thing that I’m running dry, but it’s also rather inevitable.

For the past three years I’ve been thinking about work that isn’t actually my own. I have deferred my own ideas about projects to those of my PI and we have primarily pursued paths that he has wanted to pursue.  This was great for showing me the ropes, and showing me how to think about fMRI within Psychology, something I have been employed to further here in St. Andrews, but it has also lead to this rather awkward moment of transition.  I now have to build up my own head of steam, run my own behavioural pilots and read other people’s’ articles with my own research agenda in mind.  Of course, I was doing this when in St Louis, but my livelihood didn’t depend on it.  Now it does.

So, I’m ploughing on with behavioural projects and hoping that forcing myself to think will lead to better thinking (after all, your brain is a muscle isn’t it? gah!).  I’m also considering a couple of more contrived mind-hacks to nudge the process along:

1) Read journal articles at a minimum rate of 1/weekday.

2) Design an experiment I could run at a minimum rate of 1/week.

3) Blog at a minimum rate of 1/week.

I’m not sure if I’ll follow through on these, or whether they’ll be any help if I do, but I’m going to try.  I can’t afford to stay barren for too long.

We arrived in Scotland, as planned, in September and have spent the last month settling in to our new surroundings.

My first few weeks as a lecturer have been hectic.  I still don’t have any computer equipment at work, which is making accomplishing anything substantial a tough task.  An unexpected complication of my lack of computing facilities was the knock on effect it had on my ability to engage in the bureaucracy and form-filling that I knew would take up much of my time.  These tasks are rendered even more complicated without a printer, and resulted in me having to pay the local public library a visit in order to use their facilities.

Budget 2010
Image by The Prime Minister's Office via Flickr

Amidst all my frustration at not being able to hit the ground running, I know I am very lucky.  I have landed a permanent position at one of the most uncertain times for British Universities.  Talk in the corridors is of the 80% cuts to teaching, significant cuts to research and abolition of capped tuition fees that are expected in tomorrow’s Comprehensive Spending Review.  The coalition government is extricating itself from the higher education system and this will have inevitable ramifications; in the form of university closures and privatisations.

I am lucky and I have to hope that I am also lucky when it comes to getting grants.  Research councils will have their budgets slashed and there will be huge demand for what little funding they can make available.  fMRI research certainly isn’t cheap, and if I am going to carry on with it here, as my job title ‘Lecturer in Neuroimaging’ would suggest I should, I am going to have to secure external funding pretty soon.

Tomorrow will be tough in anticipation of the lean years ahead.  Nevertheless I certainly won’t be the hardest hit by the cuts, and for that I am thankful.

Whilst Windows easily copies lots of data, it struggles when you ask it to copy lots and lots and lots of data.  Teracopy is a neat file copying utility that provides peace of mind as you transition from copying gigabytes of data to terabytes of data.

In order to get my fMRI data from St. Louis to St. Andrews, I have embarked upon the somewhat arduous task of copying everything to a portable hard-drive.   After a few attempts that ended in the failure to copy a file or two, seemingly at random, I lost faith in using the standard drag-and-drop copy in Windows, and searched for alternatives.  The command line option seemed fastest, but I didn’t want to bring the server down for everyone else for a few hours whilst I did my copying.  Then I found Teracopy.

A picture of TeraCopy
Teracopy in action (Image via Wikipedia)

Teracopy (freeware) is a straightforward utility that improves upon the Windows interface in a number of ways.  Copying is (apparently) faster and it certainly seems more reliable than the standard Windows approach.  One very nice feature is that it allows you to pause and resume your copying for when you need to free up system resources temporarily.

download Teracopy

So far I have copied close to a terabyte of data onto my portable hard-drive with no problems.  Now all that remains is to check it all with another utility (Windiff) to make sure all my files really did get copied successfully, and to actually transport my hard-drive without banging or dropping it.

Typical fMRI brain scans take a 3D images of the head every few seconds.  These images are composed of lots of 2D ‘slices’ (usually axially oriented) stacked on top of one another.  This is where the problem of slice acquisition time rears its head – the problem being that these slices are not all taken at the same time, in fact, their collection tends to be distributed uniformly over the duration it takes to gather a whole 3D image.  Therefore, if you are collecting a 3D image comprising 36 slices every 2 seconds, you will have a different slice collected every 1/18th of a second.

2D slices (left; presented as a mosaic), acquired at slightly different times within a 2s TR, that make up a typical 3D image in fMRI (right; shown with a cutout)

If you’re worried about the effect of this fuzziness in temporal resolution on your data (and there are those who don’t), then it can be corrected for in the preprocesisng stages of analysis.  Of course, you do need to know the order in which your slices were collected to correct for the ordering differences.

Finding out the order of slice correction is not as easy as it should be.  On the Siemens Trio scanner that I use, it’s straightforward if you have an ‘ascending’ (bottom to top, in order: 1, 2, 3, etc.) or a ‘descending’ (top to bottom, in order, 36, 35, 34 etc.) order of slice collection.  However, if you’re using the ‘interleaved’ order (odd slices collected first, followed by even slices), it’s not immediately clear whether you’re doing that in an ascending (1, 3 5… 2, 4 6… etc.) or descending (35, 33, 31… 36, 34, 32… etc.) interleaved order.

I found out that I was collecting my slices in an interleaved, ascending order by asking the MR technician at the facility.  But, if there was no technician to hand, or if I wanted to verify this order myself, I would be very tempted to try out a method I found out about on the SPM list today:

Head-turning research (links to poster at a readable resolution on the University of Ghent web-site)

The procedure, devised by Descamps and colleagues, simply involves getting an fMRI participant to turn their head from looking straight up, to looking to one side during a very short scan.  The turn should be caught in its various stages of completion by the various slices that comprise one 3D image, allowing the curious researcher to figure out the slice acquisition order crudely, but effectively.

I enjoyed how connected to the physical reality of our own bodies this procedure is.  It reminded that these tools we are using to make inference about cognition are tied to our bodies in a very tangible way.  That is something I often forget when pushing vast arrays of brain-signals values around in matrices, so it’s nice to be reminded of it now and again – I’d certainly rather be reminded like this, than by having to discard a participant’s data because they have moved so much during the a scan as to make their data useless!