Apparently Thursday was #DayofScience. To celebrate I thought I’d share a couple typical if my typical ‘days of science’.

Experiment day:

July 13th was actually a specimen scan day so the schedule is *quite* fresh in my mind as I write this.

3:45 a.m.

Wake up (*yawwwwwn*), drive to work with radio blasting & careful eyes out for early morning deer trying to cross the highway.

4:30 a.m. – 7:00 a.m.

Arrive at medical center/research center. Clock in, change into scrubs, head into cadaver lab and prep specimens for magnetic resonance imaging (MRI) scanning (i.e. put in labeled biohazard bags and try not to let them leak all over)

Meet technologist at scanner, get protocols set up, eat bagels while magical physics makes images

7:30 a.m.

Pull up images, freak out because artifact screwed up the one image we didn’t check on scanner before ending the session


Wrapping 😦      (The bright blob near the bottom is actually the top part of the shoulder, it shouldn’t run into the dark shapes of the scapula and humerus. MRI can use the phase of the molecule’s spin as a localizer by varying the magnetic field, and thus the resulting spin frequency, over the length or width of an image. Different frequencies makes the spins in different locations hit different phases of the spin at the same time. Here the MRI scanner got confused about the pixel location because the location-specific-phase for the upper and lower pixels in the image were the same due to inadequate phase range, so the computer thought the pixels should be in same location & overlaid them. Not helpful.)

7:30 a.m. – 9:30 a.m.

Talk to radiologist, technologist, research assistant, surgeon; get make-up scan slot squeezed in

Re-prep specimen, lug downstairs after wrapping *very* carefully so as to not freak out patients, get scanned, lug back upstairs

Get images off PACS (picture archiving and communication system), check images, sigh with relief because they look ok, let research assistant and surgeons know we’re ok to move forward.


Better MR image (left) next to CT image of same shoulder (right). No weird wrapping this time!

9:30 a.m. – 11:00 a.m.

Wait for surgeon who’s doing the research surgery to get through a morning case. Eat lunch while working on an end-of-year department summary.

11:00 a.m. – 1:00 p.m.

Discuss surgery with surgeon, find out he needs measurements from CT, run down to CT to talk to radiology tech, get 3D volumes, run back upstairs, find out 3D view angles aren’t quite right.

1:00 p.m. – 2:00 p.m.

Coordinate to get radiologist and surgeon to talk to each other, finally succeed and call surgery off in order to allow time to get measurements, firm up research plan.

Reduce frustration about delay by getting a hot cocoa.

Put shoulder specimens back in fridge, change out of scrubs. Mourn loss of clothing with real pockets.

2:00 p.m. – 3:00 p.m.

Come up with way to do the measurements in Mimics with more adjustable volume rendering, send examples to surgeon for approval.

3:00 p.m. – 3:15 p.m.

Meet with director of another department, discuss collaborative research projects.

3:15 p.m. – 5:30 p.m.

Work more on research presentation, emails, a few other small tasks.

Talk to PI about an industry project proposal.

Realize I forgot to eat my afternoon snack when my stomach cramps so hard I feel slightly ill.

5:30 p.m.

Head home!!! Shirk actual dinner making duties in favor of heating up pasta and sauce-from-a-jar with husband, who also worked a long day.


4:30 a.m. versus 4:30 p.m. after wayyyy too many trips up and down the stairs

Normal, much more relaxed day:

7:00 a.m.

Arrive at work, clock in, check email

Grab large coffee (yay!) from hospital cafeteria

Chat with PI briefly in break room

8:00 – 9:00 a.m.

Work on PowerPoint presentation for PI

9:00 a.m.

Fill out some IRB paperwork

Bug PI for IRB paperwork signatures

Scan/mail IRB paperwork

Re-print and scan/mail at least one piece of IRB paperwork because I invariably miss something…

10:30 a.m.

Snack time! First snack of the day while starting some Matlab analysis

Debug code, run code, look at the lovely resulting data plots

12:30 p.m. – 1:00 p.m.

Lunch, either with coworkers or at desk with a book

1:00 p.m. -4:00 p.m.

Work on some image segmentation on Mimics, manually tracing regions of interest in MR or CT scan images on touchscreen

Grab a second (smaller) coffee and afternoon snack

More Mimics!

4:00 p.m. – 4:30 p.m.

Meet with researchers from another department to go over a collaborative project

4:30 p.m. – 4:50 p.m.

Send out more emails, wrap up work

Make to-do list for next day

5:00 p.m. Leave and go running 🙂



More specifics – why is it especially challenging for *me* to come up with viable research ideas in my new situation?

I’m hoping the answer to this question isn’t “I’m an idiot with no original thoughts.” That would be…unfortunate 😛

Ok, so I think there a actually few external factors. First, I’ve decided, once again, to shift fields. I’m shifting with the broad orthopedics research umbrella and will be applying many of my grad program skills (writing, Matlab image processing, Gavin some clue how joints and cartilage work, etc.). However, my shift into the imaging sub-field (MRI, CT, etc.) means that there is an overwhelming amount of learning to do.

First, I need to quickly get up to speed on what’s been done and what’s possible – both in general and with our available resources (equipment, participant recruitment, technical expertise, funding, collaborators, personnel, etc.) I’m doing a lot of extra technical reading about the techniques that we use and taking in everything I can. There are SO MANY ACRONYMS :-0

I’m getting buried in reading (it’s all so interesting! But I need to figure out how to focus it…) and am only getting a small glimpse so far of who’s who in the literature. As I was completing my thesis I was finally feeling like I could list major players and their specific research focuses in my specific master’s work research area (fatigue wear in joint replacement components, behavior of the polyethylene that I was simulating).

Now I’m looking at an entirely different pool of researchers and haven’t yet seen enough papers by the same groups/authors to start making those connections. Although I didn’t usually limit my searches to specific authors or groups, seeing the continuity between advisors, their students, and various collaborators gave me a context to frame a lot of the literature that I saw, and a good idea of who would be coming out with the studies suggested in existing papers.

In addition to shifting sub-fields, I’ve also moved into a slightly different type of research. The institution that I’ve joined is focused on applied clinical research, which means we are more focused on finding and solving specific, immediate problems than just exploring. My thesis project was in engineering, which is also fairly specific-existing-problem-and-solution focused, but it was also a little more open-ended and definitely not clinical except in a very big-picture way.

As a non-clinician working on clinical problems, it is tough for me to identify problems that are more than merely interesting – they also need to address a clinical problem and take efficiency, feasibility, cost, and patient compliance into account. I keep coming up with interesting ideas, only to realize that the slight benefit of extra information may not actually improve treatment over the existing diagnostic techniques once time and cost are taken into account. I’m gradually figuring out how to balance this based on the previous and current work being done in my department.

I’m definitely looking forward to becoming more involved with our clinician investigators and collaborators and gaining access to their insight into the most pressing problems and how the proposed solutions compare to the existing methods of addressing these clinical challenges. I have a feeling I may get knocked down a few pegs, but I’ll certainly be learning and growing in the process!

** Any suggestions for strategies to overcome these challenges are more than welcome 🙂 **

Challenge of the week: synthesizing research ideas

I’ve been working as a research engineer in my new job for a little over a month. It’s been a bit of a crazy transition, as the only coworker physically located in my lab left the week before last to continue a medical career and my other colleagues are both long-distance employees. I’ve suddenly found myself alone in the lab in a new field, with new protocols to understand and names to learn and hospital-maze hallways to navigate. My colleagues are only available by email…and in different time zones for added fun. My boss, RadPI, is generally busy with clinical work and isn’t really available for small-detail chit chat/questions.

Overall, very exciting but also anxiety inducing. Last week my anxiety levels got another boost when RadPI casually mentioned that I should be coming up with some research ideas, as the lab work is now kind of my ‘baby’. My initial reaction was panic – oh dear lord, what if I fail and my metaphorical baby DIES!!!! Aaaaahhhhh!

Guess what’s not really helpful for systematically reviewing the literature in order to identify and analyze gaps in the field? Utter panic! So, I (sort of) calmed down and came up with a little more of a plan. 

First, I would look at the current protocols that we were considering utilizing and see how others had used them and whether they might be applicable to areas that our lab has been focusing on. Next, I would discuss any ideas that I had with my colleagues and see what ideas they had for future projects. 

I spent the next couple days absolutely buried in PDFs, sorting through new material and trying to gain a better understanding of the benefits and limitations of the various cutting-edge techniques.this let me develop a few ideas of my own and a bit more technical knowledge before switching over to looking at future work that had been proposed by previous members of the lab.

I was delighted to find a giant file folder stuffed with notes, annotated PDFs, and proposed project outlines. After getting partway through it and realizing several projects were half done or completed, I realized that I needed to be more systematic and actually go through and organize the notes to correspond to completed, in progress, and future work. 

This crazy organizing process, which took a full day of paper-cut risking work, made me realize that running or working in a lab with short-term staff, such as grad students, could be an absolute nightmare in terms of continuity if notes weren’t well-managed and projects to place in many lengthy stages. From my past experiences, the PI/head of the lab generally knows the big picture for each project, but passing down details/what worked or didn’t/cool side project ideas is extremely tough once the lead on that specific project leaves the lab…

I was lucky enough to stumble on the folderand its valuable cache of notes, which gave me much more insight than the electronic file that just listed the projects by title with no details as to the inspiration, potential pitfalls, or tangents. Fortunately I was able to whittle the hard-copy and electronic work down to a single, but more detailed, list while incorporating my ideas and some suggestions from my lab mates.

Now I just need to pull myself out of my nest of PDF pages and discuss all these fabulous ideas with my PI and long-distance lab mates! Interestingly my last few days of article reading and idea synthesis have been some of my most exhausting work days thus far…time to crawl in bed and give my brain some much needed rest.

*Tomorrow I’ll discuss a few specific challenges and field/lab-specific difficulties that I faced when trying to come up with the research questions themselves*

Human subjects training

I completed my annual Protecting Human Research Participants training today. Clinical research involving human participants has resulted in invaluable advances, but has also been scarred by horrifying abuses and cruelty in the name of medicine and science. PHRP training is intended to provide researchers with a background in human subjects ethics, as well as familiarity with the NIH and Health and Human Services regulations and the role of Institutional Review Boards, or IRBs.

The training itself is not exactly thrilling, consisting of lots of regulation-reading, multiple choice quizzes, and a few case studies. I’ve heard many researchers groan about the whole process, about the IRB requirements, and the general beaurocracy involved in human subjects research. After all, it’s kind of a pain, and we all know better than to treat our participants in unethical ways, right? 

However, the regulations are actually more complex than just ‘common sense’. For example, tissue taken from living donors (even as surgical waste) does count as human subjects research, but that tissue or data about it may be used for later studies without informed consent IF there is adequate anonymization. Minors (under 18) may or may not be subject to additional regulations as ‘children’ depending on the legal age for consenting to various medical treatments in different states and the regulating agency. But, from my understanding, for NIH funded studies anyone under 21 is classified as a child. There are seemingly endless rules in place with the overarching goals of promoting respect, beneficence, and justice.

 The research that I’m currently becoming involved in employs widely accepted interventions and, as such, is less ethically complex than research that involves higher risk to participants. However, the main ethical principles are no less important even in ‘minimal risk’ intervention studies. 

For me, the most motivating part of the PHRP training is the history section. It provides a painful walk through the abuses put upon human subjects, particularly vulnerable populations such as prisoners, institutionalized children, minorities, and those with too few socioeconomic resources to fight intimidation, deceit, and coercion. Many of these maltreatments were probably not fueled by simple evil or maliciousness, but by some twisted logic in the pursuit of ‘successful’ research with no consideration for the cost to those involved. The current system of IRB review is not infallible, but at least provides a relatively objective outside interpretation of whether the benefits of the proposed research truly outweigh the risks to the participants. 

I’ll be writing more on this just as a way to think through the concepts & become more familiar with the regulations, and to cover some current happenings that bring certain aspects of the requirements for respect, beneficence, and justice (and the actuality of those principles in clinical research) to the forefront. 

** I’ve been a research participant multiple times in studies requiring and exempt from formal informed consent/IRB recruiting procedures (exempt studies kind of crack me up since I’ve been recruited for two by being essentially pounced on by desperate PhD students roaming the halls of the mechanical engineering building in search of female participants). I do feel like I’m at an advantage over many participants as far as protecting myself, since I have some research background and am generally participating in research conducted by my peers/fellow students/lab mates and don’t feel as much intimidation as I might have if I’d been interacting with an unfamiliar or authority figure.

Things I learned from Medscape and Google Scholar at work today…

1) Cordless power tools don’t mix well with implantable cardioverter-defibrillators.

2) There is a procedure called “tongue suspension” for treating sleep apnea that involves screws and lots of surgical suture. Google image that for some disturbing pics 😛

3) People with mono shouldn’t take Amoxicillin unless they want lovely measles-like rashes. I really want to know how that works…

4) If you jump down the cited-by rabbit hole you can get from random-paper-about-antibiotics to case-report-of-awkward-mouth-bruises-of-questionable-origin in about 10 papers :S

Good times…

Things I have learned while thesis-ing

Getting this thesis wrapped up is kind of kicking my ass. I *like* writing and I actually really enjoy working on figures, but the seemingly endless sets of read-revise-read-revise-send for feedback-freak out-revise-revise-revise are killer. However, I’ve come up with a few habits that are helping keep me sane:

1) Just do a dang outline.

I abhor making outlines. Something about the formal, roman-numeral outline just drives me bonkers – tedium mixed with tough brain work all in a ridiculously tidy package. I can generally get a 10 page paper out of a very loose outline, my set of figures to keep me on track, and some post-writing revision. However, a 100 page document is a drastically different story. I used a loose outline for my 1st draft and am now paying for it. I’m currently making a new (much more detailed!) outline to go over with my advisor to reduce redundancy and improve flow.

2) Write when you can…and take breaks!

I’ve realized that cramming a solid 8-10 hour block of writing in leads to getting lots of words on paper…er, screen, but also results in about ¼ of those words being “garbage words.” Too much fluff & filler, not enough sharp, concise statements. I work best from about 8-11 am, 2-4 pm, and 8pm-11 or midnight. Kind of a silly schedule but hey, if it gives better results it’s totally worth it!

3) Stay positive!!!

Every time my advisor sends feedback I take a deep breath and then dive in. I inevitably find myself muttering angrily under my breath and glaring at the solid screen of comments and track-changes. But then I take a walk, come back and find a few easy-to-address comments, and try to look at the tough comments in a new light. My advisor and I are working towards a common goal – technically accurate and compelling thesis! So after looking through the revisions I’ve been making a habit of sending him a “thank you for the feedback, specifically blahblahblah” email before diving in to actually fix/add stuff. Somehow the act of saying “thank you” actually shifts my attitude more towards the grateful and further from the “What is this guy thinking?!?!? Ack, I’m never going to finish >:[” mindset. Copious quantities of chocolate also help 😉




Oh, hey there…

Just realized it’s been a week since I last posted.  Oops – I hope none of my *billions* of readers have pined away without my brilliant musing to sustain them 😉  

Anyhow, I was plenty busy without sending any of my bloggy drivel out into the internet ether.  I got in a solid 20 hours on research and 30 hours of teaching/grading/prep work during the week and a short thesis outlining session in over the weekend.  Research has been frustrating lately – long story short, software is not behaving due to corrupted files.  At least it’s not due to something I did wrong…although maybe that would make it easier to fix.  I’ve been fighting this issue for several weeks and spent this week going back and forth with the support folks.  Alas, the issue wasn’t resolved as of Friday afternoon.

I have no desire to further raise my blood pressure & cortisol levels tonight so I’ll stick to talking about the (much more successful) running portion of my week.  I got in a second week at ~16 miles total, plus a couple hours of cross-training/lifting.  Oh, and MountainMan and I got a wobble-board so we’ve been getting in some painful little foot rehab sessions on that.  I’m totally kicking his butt in the single-leg squat balance competition that he doesn’t know we’re having 😉  

I found out that the path over at Liberty park is relatively clear and got in some nice “long” runs (a measly 4 – 5 miles, sigh).  Besides the paucity of ice/snow, the park is pancake flat and has rows of beautiful towering pines that shelter the running path from the road noise nearby.



I was lucky enough to get MountainMan to join me today, although he was less pleased than I was about the fact that it was pouring rain.  He was a good sport however and we had a nice jaunt through the mostly empty park.



This guy rocks my socks 🙂  Also, my phone camera lens fogs up quite interestingly in the rain 😛

The aftermath of 5 miles?  Some nicely mudded calves and shoe-laces that closely resemble drowned worms:



Here’s to adding a couple more miles next week and, fingers crossed, some better news on the research front.  Lastly, good luck to all you winter-weather braving runners out there!  We got this 😉