Week 6: Calm Before the Storm

This week was a little less eventful than the previous ones, though some new assignments I've now been given promise an eventful next few weeks. :)

Also, shoutout to BASIS Scottsdale's Science Bowl A Team for winning the regional tournament. Good luck in DC, guys!

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Presentation
I should clarify, as it's been a source of confusion, "CORE Lab" is a name both for the new method of lesion measurement as well as the lab the method is being tested in.

This in mind, several important members of the CORE Lab showed up at our weekly meeting to, among other reasons, listen to the presentation I mentioned last post. It was mostly the same as what I typed up on last week's post, except with added data, conclusions, and spreadsheets as source material. They seemed visibly impressed, which bodes well for the scope of work I'll be permitted to get involved in for the last four weeks.

Bring It On

In any case, I've begun making my presentation for my SRP, as I have enough somewhat scientifically sound conclusions to do so.

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Ah, Clinic Lectures, They Never Fail to Amuse
I attended two lectures this week.

Lecture 1
This lecturer discussed different diseases which looked similar through CT scans, and how to tell which a patient had. I was actually able to follow along rather easily, absorbing as much as I could. However, nearing the end of the 45 minute block, our lecturer suddenly announced "Pop quiz!" in the most mock-high school teacher way possible. Wonderful.

A scan was shown on the board along with four multiple choice options as to the condition the patient might have, and random people were called out to give their thoughts. The fact that the first three people had gotten their questions right didn't help when the lecturer called on me for the fourth problem. I stared at the amalgamation of black-and-white abdominal body parts before me and thought, long, hard, and fruitlessly. Well, not entirely so, for I realized option D was a chest condition, and thus (hopefully) not applicable. I sighed, and picked C. What do you know, I was right. ^-^ To give you an idea of how much of a guess that was, I don't even remotely remember the question or what the answer C was.

Lecture 2
This one started off innocently enough.

"We will be discussing the minute differences between PET scans and CT scans, and then move on to analyze the advantages and disadvantages of PET-CT hybrid machines." Great! I already knew a fair deal about both scanners, so I wouldn't be a leg down during this talk. So I thought. Apparently the key word in the above statement was "minute".

This guy launches into collegiate level particle physics, slamming down more equations in one minute than I had committed to memory in all of honors physics. I was mentally paralyzed, unable to react in any appreciable manner. So I slowly and awkwardly ate the vanilla pudding I had brought with me from the clinic cafe, nodding once in a while to give my temporary teacher affirmation that I knew exactly *cough* none of *cough* what he meant. It didn't help that there were less people than usual attending this lecture, around 5 as opposed to the usual 10 or so.

At around the halfway point, I heard and saw something I understood. "This is a picture of a PET-CT hybrid machine."

Then it was back to attack of the variables for the last 20 minutes.
'blahblah... neutrino... talktalk... gamma delta of the particle collider... so on so on... I like cantaloupe...photon-gluon combination...'

me

There was actually a lecture I attended yesterday in which I showed up the lecturer at one point. It wasn't a big deal, but I found it funny regardless. Tune in next week to hear that story ;)
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Elevator
I got on the same elevator I always do to go up to the Mayo cafe and grab some grub. But I pressed the 'close doors' button twice and nothing happened. Confused, I hit it a third time, and the doors started closing. Right before they could finish closing though, the elevator started moving up, jerked to a stop, waited a few seconds, and then resumed. It was disorienting and somewhat curious. Yeah, that's it. I know, these events are boring, but they're all I've got haha

Unrelated Gif Because Why Not

I wish all you readers a wonderful, eventful week. See you next time!

Week 5: Revelations

Hey guys! This week would have ordinarily been spring break, but I took my one week break on the first week, so I was to show up at the clinic as always. Funny thing, I completely overlooked this until the morning of.

jkjk this internship is awesome and I love it ^-^

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This week, I have been analyzing my spreadsheet using Excel analytics to see any trends I can find between Clinical and CORE Lab data. As a quick recap, the commonly used and heavily physician based ‘Clinical Trial’ process uses the observations of field experts in lesion size measurements and data collection. The experimental and heavily computer software based ‘CORE Lab’ process uses automated measurements and reports to record lesion data. I am trying to determine which is more effective as a standalone method for physician use.

Here are some of the basic stats and conclusions I came up with. Again, I can't post the actual spreadsheets I made to crunch these numbers in the interest of patient privacy. Do you like the font? I think it looks very analytical.

How many lesions had core lab measurements (for at least one dimension): 115/272

How many lesions had clinical measurements (for at least one dimension): 76/272

How many lesions had both measurements (for at least one dimension): 64/272

Core Lab to Clinical Ratio: 1.51:1

Including “Present” - Clinical: 87/272 - Core Lab: 265/272 - Ratio: 3.05:1 ("Present" refers to lesions marked as existent but too small to bother taking measurements for, and only just big enough to take note of location.) 

y = 0.6948x + 0.5064
R^2 (coefficient of determination) = 0.616 

y = 0.7137x + 0.4033
R^2 = 0.664

Long axis and short axis refer to the dimensions of different lesions, in centimeters. These graphs use a linear structure, though I also have logarithmic, exponential, power, etc.

Quick conclusions:
-Doctor mostly independent of how much quantitative information provided. On the other hand, reports may change style according to referring physician.

-Only one CHESON report.

-The Core Lab had a lot more “Present” lesions w/o numbers attached than the Clinical Trials, even accounting for the data amount disparity between them.

-The Clinical Reports had a lot more human analysis and comments in general than the Core Lab Reports, as seen by my “Clinical Comment” addition to the columns in my spreadsheet.

-Main types of cancers? Leukemia, Lymphoma, and Breast Cancer (often metastatic).

-Bi-Dimensional Reports often had similar and predictable lesion descriptions, such as Rt. Hilar, Lt. Axillary, etc. On the other hand, RECIST and CHESON reports had varying names and descriptions for every single lesion, as well as specific designations such as NT01 or T02.

-Only two lesions (from the same set of Core Lab data) ever had Diameter Product listed, counting both Core Lab and Clinical reports.

-Excepting a few outliers, the Clinical numbers tend to match up rather nicely with the Core Lab numbers, indicating an expected level of accuracy.

-Bi-Dimensional Reports have a lot more quantitative data recorded in general compared to RECIST and CHESON reports.

I am currently working on an in-depth analysis promising more numbers and more refined conclusions. 

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Operation Overlord (Tempest)

At one point some new monitors came into the lab, and I was tasked with setting them up, as well as dismantling some old computers completely to make room for them. The first one took quite a while, but once I got the hang of it, I was able to finish setting up most of them pretty quickly. That is, until I reached the second - to - last computer. It had the name, I kid you not, "Overlord Tempest" and a some fantasy knight with a red cape emblazoned on the box.

It does look pretty cool, gotta admit.

Name aside, this thing was HARD to set up. Not only was the monitor heavy enough to crush a blue whale, but it seemed like there were enough wires to trip every person on the planet at least once. Needless to say, I wasn't making very much progress.

When my supervisor Christine walked in, I asked her if she could offer me any assistance. She smiled and said, quote, "The difference between a challenge and torture is knowing when it'll end." Gee, thanks. It also should be noted that I had no clue when I would finish setting this thing up haha

Eventually, after graciously accepting the help of "George" (whom you may remember from the Quest for Edward) I was able to get everything the Overlord threw at me functional. 

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The Case of the Missing Lecturer

I attended a lecture last Tuesday. The lecturer never showed up. I thought that was pretty big news. Others in the room told me it was a commonplace occurrence. Huh.

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And finally this week, I was told that I would get an opportunity to speak at next week's meeting for 5 minutes on anything related to my project. Normally, I'm just allowed to listen in, so this is big. :)

Thanks for reading! Hopefully I can get next week's update out in a more timely fashion.

Wonka please, I have follower base nearing double digits. You're just jealous.

Week 4: Conference Calls and Lemons

Hey! Hope you had an absolutely fantastic week guys! I'm back with an update on how things are going at the ol' clinic.

Everyone Reading This

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First, as always, an update on what I'm doing academically.

Interestingly, I'm already done with the work my supervisors prepared for me, both to answer my research question and to help them with documentation. That is to say, I've completed the first version of my spreadsheet of Core Lab and Clinical Trial comparisons, complete with ungodly amounts of patient data. Now I'm making graphs and forming conclusions out of the data. (Something which Excel is helping me out with WAY more than I initially imagined.) Once I've studied my graphical trends enough, I should, in theory, be able to answer my question of which method (Core Lab or Clinical Trial) of data collection on lesions is more effective and/or more efficient. But am I satisfied with that? Ha! No. My two most recent days on-site I've been asking for other jobs to do, so that I may tie then into my SRP somehow.

One interesting job I got involved OsiriX, a high quality photo storing and editing software. I had to censor patient data for reports and ultrasounds before they became 'public domain', so to speak, for doctors everywhere to use in teachings and presentations. The craziest thing is, I recognized one or two of the names I came across from earlier data collection. Small world. Anyway, at first, progress was slow, for I had little to no idea what I was doing. But I'm nothing if not a software junkie, and I quickly learned the in's and out's of what I could do with OsiriX, to the point where I was flying through the pictures 10 times as fast as before. Add in the fact that I started listening to Two Steps From Hell on my phone, and I was nigh unstoppable for upwards of two hours.

While I was censoring data, I couldn't help but notice some big, bold text at the top of the screen, reading: "NOT FOR MEDICAL USE WITHOUT A LICENSE. CLICK HERE TO BUY LICENSE." I turn to my supervisor Kelly.

"So when do you plan on buying the license for this?"

"Oh...y'know...sometime." Heh.

please tell me someone gets this joke

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Conference Calls
I was allowed to attend a meeting again this week, except this time we had a phone to have another group speak up during the meeting despite being elsewhere. But first we had to set up the conference call. And judging by the look everyone was giving each other, this was something no one wanted to do. I almost felt a game of "onetwothree not it" coming on, when-

"Ugh, fine, I'll do it," said my supervisor Christine.

She brings back the telephone and dials in a number.
"Please enter the confirmation number." She does that.
"Please enter the conference number." She does that.
"Please hold." She holds.
"If you want to _____ press 1. If you want to _____ press 2." It prattled on for 9 numbers. I quickly realized that one had to wait till it finished before punching in a number.
"Now re-enter the confirmation number." She does that. We have successfully set up the call. Someone also told me afterward that if you messed up even one number, you had to start over. Ouch.

During the call everyone was getting pretty excited over what appeared to be a possible grant for the CORE Lab and all its members. Apparently there was a 50% chance they'd get the grant over another department of Mayo, and this all depended on a higher power's judgement. So essentially, we had to convince this higher power how awesome we were. Someone brought up NVidia (the graphics cards both many high end video games and many medical imaging softwares use), citing that the higher-up we were appealing to was a gamer. I failed to put 2 and 2 together, but it somehow caught on with the rest and within 5 minutes we had arrived at the most slippery slope known to mankind.

Essentially, since we used NVidia graphics cards for lesion scanning and the same cards were used for gaming and the one with the authority to give us cash money was a gamer then it follows that if we mention our liberal use of graphics cards then he'll like us and give us said cash money. QED.

And that's exactly what we did.

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Lemons
While I was working, someone whom I didn't know walked into the room, continued walking straight up to me, and held out a bag full of lemons. And these lemons were, in a word, gigantic.

Ok, so they weren't that big, but you get the idea.

"Would you like a lemon?"

I cautiously picked up one of the smaller ones and thanked him. I felt better when he offered them everyone else in the room as well. It was still completely random though. I haven't seen that guy since.

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And finally, my supervisor Kelly had her last day at Mayo last Tuesday. She found another job that she wanted to take up, so she resigned her spot here. Goodbye and good luck Kelly! I will miss your ever-helpful demeanor towards me, but more than that, I will miss your massive snark. Stay chill. :)

Week 3: Moving Up the Ranks

Note: Sorry for the tardiness of this post. Me at 4:00 AM in the morning a few days ago couldn't distinguish between the "Publish" button and the "Save" button. Only now did I realize. Anyway, expect the next post this Saturday. I have some very...interesting stories to tell. :)

Week 3: Moving Up the Ranks

Hello again! I hope you all are having a wonderful day today. I've got another week full of the mundane and the exciting to share, so without further ado, let's jump into it.

You Bet It Is

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I'm finally finishing up one of the first main Excel spreadsheets with a full set of live patient data! It took a long time, and was quite tedious at points, but the results show. Over 30 panels across and 300 panels down, all filled, it is truly a giant of a chart. Unfortunately, due to the fact that there is patient data unreleased to the public for confidentiality reasons, I cannot show you guys any part of my spreadsheet, at least right now. I can, however, give you the variables I list on the x-axis.

A typical lesion on a typical patient will require a variety of factors to be logged. These include, but are not limited to: Patient Name, Patient #, Patient ID, Date of Birth, Date of Service, Lesion #, Lesion Type, Lesion Description, Possible Diseases, Data Logging Type (RECIST, Chesion, Bi-Dimensional, Tri-Dimensional, etc.), Long Axis, Short Axis, Depth, Volume, Image #, Series #, Comments, Evaluation, IRB Index (basically which folder the patient is put in), Priors, Visit Name (Baseline, Followup 1, Followup 2, etc.), and many more.

(basically if every variable that has ever existed got together and threw a party)

These all must be logged for both the core lab patients and the clinical patients, as one of the main focal points of my SRP is to determine which of the above methods of lesion identification and classification is better.

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Moving on, I attended two lectures this week. The first discussed radiology software on mobile devices, the second focused on cystic fibrosis and the kind of technology Mayo was using to fight it.

Lecture 1: Apparently the first time the lecturer's colleagues proposed adding software such as XOsiris and Mintleaf (both of which are used to view and edit high-rez images of medical scans, among other uses) as an app to the first IPhone, only recently announced by Jobs at the time, they were quite literally laughed out of the room. (So I hear, anyway.)

"There's no way a PHONE can properly run our top notch software without crashing!" Oh how wrong they were. As the IPhone and IPad went on to become the international sensations they are today, the technical specs increased dramatically with every update. Now, an IPad can run most software as apps better than actual machines/computers on Mayo's (and other hospitals') sites designed specifically to run those softwares. Iphones are almost as good. Interestingly enough, Android devices tend to have problems, so most medical professionals don't use them on the job. *cough* Shrey Gupta *cough*

The lecture went on to talk about levels of security and accessibility and how mobile devices could also use these in needed apps. On the topic, I currently have an unofficial clearance level of 2. According to the lecture, level 1 entails moving data, level 2 allows for viewing data, level 3 permits limited editing of data, and so on. One of my supervisors, Christine, is trying to get me the equivalent of level 3 access due to my good work and general helpfulness thus far. Good, good, I am moving up the ranks. First Mayo, then the world.

cheesy forcibly inserted meme is cheesy

The second lecture about cystic fibrosis mentioned the use of NVidia graphics cards to help patient scans be of top quality. I perked up when I heard 'NVidia', for I knew the same graphics cards to be top notch for PC gamers. There's actually a really funny story related to this that happened at a Mayo conference I attended, but I'll tell it on the next blog post, you'll see why.

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And finally, let's talk about what I'm dubbing "the Quest for Edward".

My supervisor Christine told me and an ASU Graduate Student whom we'll call George (he's awesome, btw, he just looked kinda bad at one point in this story so I'm not giving out his real name) to go find this guy called Edward. Apparently he was the one who shipped a server Mayo needed to our Scottsdale clinic, so he was the one who knew where we could find it and carry it in. All we had to go off of was a phone number.

So we called him. No response. Fantastic.

We starting combing Mayo asking everyone in the most awkward ways where 'Edward' was.

"Ah, excuse me, do you know anyone here by the name of Edward?"

"What's his last name?"

"Uhh...he shipped a server over here. That's all I know."

"No idea, sorry." Or some variation of this.

We eventually decided to check the last few corners of the building we hadn't crossed yet, and give up if no leads were found. As we're doing so, I faintly hear Uptown Funk playing in the distance. Curious, George and I follow the music as it gets louder and louder. Finding the source, we see two individuals and a radio BLASTING the song at maximum volume. And - you guessed it - one of them was Edward. (Well no wonder he didn't hear his phone considering Spotify Top List was playing at no less than 3000 decibels haha)

And even then it wasn't over. George started asking for a server, and Edward didn't seem to know what a server was, so he started describing a package he brought in recently. Turned out, it was the exact description of what a server looked like, but it also turned out, George didn't know what exactly a server was either, because he kept asking 'for the server' even after it was described. I tried to interject to clear things up, but I was shushed.

Eventually though, everyone understood what was going on, and we got our server. Yay! :)
(ugh finally)

See you next week!