The End of the Beginning

你好! Okay, there's your Chinese. Enjoy it. :D That little phrase means hello. Congrats, you now know as much Chinese as I do. 

Well, my internship is over.

However...my time with Mayo Clinic is not. That's right: I've gotten a paid internship there! You already know what that means.

Here's to another ten weeks of more lemons, more silly lectures, more drones, more Edward, more janky elevators, more Excel, more conference calls, more proton beams, more F3, more food, even more silly lectures, more internet explorer, more Overlord Tempest, and just more of everything really.

Unfortunately, I won't be blogging about it, because I'm really lazy. But I'd like to take this opportunity to thank you guys for sticking through with me and offering your questions and comments. It really made this experience worthwhile!

All that is left is my actual SRP presentation. The gist of it is that, yes, the CORE Lab method does indeed surpass the Clinical Trial method as a form of data collection with respect to patient lesions. Wow, that's a mouthful XD

Anyway, I hope you all have a great day!

Peace Out

Week 10: The Power of F3

Guten Tag! Now you may be wondering why...just kidding, you know why. I'm using Chinese next time, by the way.

Already Better Than My Chinese Skills

This week is the penultimate in my Mayo Clinic experiences (actually, possibly not, since I've been trying to get a summer job there) and it's safe to say that most of what I had planned to do, even the side projects, are wrapping up.

And about that proton beam facility visit? Uhh...I couldn't go. Something came up. :( But I've taken the liberty to research the facility, and I'll present what I found important/interesting below.

Possibly Accurate Description of the Proton Beam Facility
The facility is one of many spread through both Minnesota and Arizona, the aggregate of which will be able to serve a total of 2400 patients annually including 250 children. (The proton beam process must be tweaked to accommodate children.) Treatment from our Phoenix facility specifically will start up early 2016.

The type of beam radiation therapy used would be the latest available, which uses quote: "spot scanning to "paint" dots of protons back and forth through a tumor." This is known as pencil-beam scanning. It offers greater control over radiation times, fewer side effects, and shorter treatment times than conventional proton beam therapy. (which is still crazy avant-garde, mind you) The machine itself, though built so that very little of it is visible in treatment rooms, is enormous, occupying three floors. Included is a synchrotron designed to accelerate protons to 60% the speed of light. Of course, the patient will feel little to nothing at all. ;)

The Power of F3
My supervisor Amy had sent me three spreadsheets, each containing patients with head, liver, and chest problems respectively. The goal was to look up each of these cases in the database, bring up the full report, and mark certain trends or conditions in those reports. For the head and chest cases the 'key words' were more varied and nonspecific, but for the liver lesions, there was one key word: metastases. (The breaking off of cancerous cells to new parts of the body.)  So all I had to do was, rather than read the report, press F3 and type in 'metastases'. I didn't read any of those liver reports, to be honest, rather, I burned through 60 of them in 60 minutes. :D

How to Make an eBook
One of the tasks I completed this week was helping Christine organize and compile 'eTextbooks' of sorts containing trial cases for people to use in radiology practice. As usual, actual patient data had to either be censored or replace with fake information.

Evolution's Role in Medicine
This was the first time I had attended a "grand rounds" lecture, where the possible subject matter was quite broad and meant for a general medically-inclined audience. And the lecture hall could seat like 200 people. And, big surprise here, most people came dressed in suits. I seriously ought to start doing that.

It is also worth noting that the talk had one of the most legit starts of any talk I'd ever listened to, with someone coming up to introduce the person who would be introducing the main speaker. No, I'm not making that up.

The actual lecture was, in my opinion, the most interesting I have been to thus far. The basic premise was that there are very few connections made between evolution and modern medicine, when in reality they are quite intertwined. And I'm not talking about some random psycho-evolution stuff or anything, I'm talking cold, hard, Darwinian evolution.

swag on

Discussed was everything from the ever increasing bacterial resistance to penicillin, to reasons NOT to take all the pills in the prescribed bottle, especially after you're feeling better. Especially interesting was the discussion of why we, or any other species for that matter, hadn't evolved resistances to specific diseases that had plagued us for as long as we've been around. The most we've gotten is a jack-of-all-trades immune system (granted, an extremely adaptive one) that isn't infallible by any means. This question led to the interesting question of why, while the bacterial diseases that have been around for eons are sharply decreasing in power due to antibiotics, mental and autoimmune diseases are increasing exponentially to match? Is it our new, chemically infested environment? Or something else?

The lecturer added a disclaimer at the end saying that none of what was postulated was set in stone. (Probably because multiple points made clash directly with popular medical thought at the moment.)

Food is Love, Food is Life
So normally lunch is super cheap at Mayo, no more than $5.50 for me most of the time. So today when I saw I had $6.00 to spare, I wasn't worried. I also saw a spare nickel hiding at the bottom of my bag, but decided not to bring it along, reasoning that I wouldn't need it. Lo and behold, there was a special today. A charbroiled Texas-style chicken burger with giant onion rings AND french fries AND a 16 oz. drink included. For $6.05. 6 dollars and freaking 5 cents. So did I go back to the elevator, up 2 floors, and to the CORE Lab to get my nickel? You bet I did.

But the real question is: was it worth it?
Yes.
10/10
would eat again

I wish I could say this is an exaggeration

Week 9: Another Quick Update AKA For Want of Stuff to Talk About

Howdy! Now, you may be wondering why I just used the word 'howdy' to open up a blog post. Well, that's because, after using 'salutations' last time, Mr. Atteberry suggested the word to me in an effort to keep with the whole "different greeting each time" thing. If you're still reading, congratulations, you've survived the worst of it.

just kidding I'LL NEVER RUN OUT OF IDEAS they'll just be really bad ideas

Anyway, this week was quite uneventful as I did more or less what I've been doing over the past few weeks, but in bulk so as to have more data for presentation. Speaking of presentation, I'm almost done with a first draft of the powerpoint I'm going to present. It asks the question of whether the CORE or clinical method of lesion data measurement is more effective and answers that question as the slides progress. The real challenge here is to incorporate all the little side projects I've been doing into my main question without having them feel forced in. Speaking of side projects... (flawless transition)

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Liver Data

The sideproject in which I'm looking through diseased liver cases from the pathology department -  to find the ones with the most quantifiable information, so that the CORE Lab can use them for analysis and cross-referencing - has yielded some results!

Through a sample size measurement, I have determined the likelihood of a case (in the total pool of 1800 cases or so) having certain statistic and/or conclusion tied to them. What I've found is as follows:

-Simply identifying the presence of steatosis/cirrhosis/other happened 1 in every 1 case, that is to say, all of them.

-Identifying macrovesicular/microvesicular damage happened 2 in every 3 cases, leaving the usable amount of cases at approximately 1200.

-Using the NAS Score (a score out of 8 measuring the fattiness of liver, the variables of which are variable themselves, but are generally pinpointed down to inflammation, degradation, and steatosis) happened 1 in every 10 cases, leaving the usable amount of reports at around 180.

-Using the hepatitic index score (a score out of 18 determining the severity of hepatitis in a patient, the variables of which are hard to pin down and thus will remain unnamed) happened 1 in every 15 cases, cutting the usable number of reports down to 120.

-Other possibly usable statistics were too janky to consider.

I defined a few of the confusing terms listed above in my last blog post, so check that out if you feel so inclined. :)

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Proton Beam Facility
Mayo Clinic is offering a tour of their newly constructed Proton Beam Facility to Mayo employees before the facility is opened to the public. A shuttle will take me there and back from the Scottsdale Mayo campus, and the best part is, time spent there will count as internship hours for the SRP (aw yeah)

It's funny, cuz you can see Excel open on his computer, and Excel has essentially
been my life these past weeks.

My assumption is that the facility will use proton beam technology to treat cancer in a more precise manner, targeting tumor cells more effectively while being able to spare healthy ones. It'll likely be quite an exciting tour, and I'll be sure to tell you about it in the next blog post!

Until then, signing off. Have a great day! (Wow my blog endings are becoming as cheesy as my openings)

Week 8: Mmm, Free Lunch

Salutations! The only reason I just wrote "salutations" is because I wanted to greet you guys a different way every blog post, and all the obvious ones like "hi", "hello", and "yo" had been taken. So there you go.

Now I know what you're thinking. "Is this necessary?" No, no it really isn't.

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In Which I Invade Other Departments

My liver research and identification from last week continued this week, and I must say I've learnt quite a lot from it. If you don't remember what it was I was trying to accomplish last week, allow me to copy-paste my explanation from my previous post, not only to give you a refresher, but to fill required blog space.

"The fields of radiology and pathology are quite interconnected. At Mayo Clinic, both departments often end up treating/diagnosing the same patient livers for different reasons. Our radiology department wanted to know how accurate our diagnoses were, so I was given access to a report database called Illuminate Insight and told to find liver reports from the pathology department that had a ton of numbers in them, so that our doctors could cross reference radiology reports to check for accuracy."

Continuing the trend of filling said blog word requirement, (even though I'll probably exceed it anyway), allow me to define some of the most common terms I came across pertaining to the liver.

Cirrhosis - Scarring of liver tissue, often a result of fatty liver. Severe cases can lead to liver failure.

Steatosis - The abnormal retention of lipids in a cell. (In this case, liver cells.) This leads to vesicle enlargement. While steatosis and cirrhosis and independent of one another, severe steatosis can lead to fatty liver which can be a strong indicator of cirrhosis. There are two types of steatosis:
                  Macrovesicular: When the vesicle enlargement is enough to push at the nucleus of the cell.
                  Microvesicular: When the vesicle enlargement is not enough to push at the nucleus of the cell.

NOS Score: A score given, out of eight, to show how diseased a liver is. There are three different factors to consider when assigning a score, which I'm not going to go into detail on. (Mostly because I don't know much about them.) The higher the score, the worse the patient's liver.

After a while I was told to go meet with Dr. Dora Lam-Himlin of the pathology department to help with whatever she required. Upon arriving I was presented with arguably the most interesting task known to humankind. Organizing files.

I kid, I kid, it wasn't that boring, I did in fact get to use software exclusive to pathology medical professionals. (Edit: for some reason these two paragraphs have a white highlight on them and I can't get it off >.< )

This actually happened. Multiple times.

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The Awkward Moment Heard 'Round the World

At, 11:30 on Tuesday, as I always do, I asked Christine if there were any lectures I could attend. She responded affirmative, adding that today's lecture host had set up free lunch. If wasn't interested then, I certainly was now. Apparently, the host was also a professor at Harvard.

The fact that he is quite the recognized lecturer from across the country is secondary.
Now where are the forks?

Ok, so here's where I should explain things before I delve into hilarity. The room where lectures are usually held has a television which is a live video feed to another room somewhere else entirely, so that, with one lecturer, two rooms can listen in.

So I walked in, and there was no one else in the room. Strange. I then noticed the buffet of food next to me and walked over to get some. And by some, I mean A LOT. See, I hadn't eaten since 4:00 PM yesterday, so I was ravenous. I took 5 burrito wraps of which I'm sure most reasonable people would have taken one or two, And so on for the rest of the food. After that, I sat down, and suddenly realized that the live video feed was rolling. Taking a look at it, I found at least 15 people, all dressed in suits, staring at me from the other side, including the lecturer. I meanwhile, was wearing casual clothing, had forgotten my clinic badge to prove I was an employee, and had half a veggie wrap stuffed in my mouth. Not to mention there was still no one else in our room. Yep.

We stared at each other for a soul-crushing five seconds before I just sat down and continued to awkwardly eat. And then (of course) other people started walking into our room.

The actual lecture was quite interesting and easy (relatively) to follow, mainly concerning recent and future technological advances in the fight against obesity, diabetes, and cancer. Many memorable concepts, all with working prototypes located elsewhere, were introduced. One was a chemical that induced neutrophils (the first cells to intercept foreign matter entering the body) to act faster than they normally would. For some reason I was unable to comprehend, the chemical was more effective on those with conditions surrounding obesity. Another technology talked about was what's known as "biomaterial gels". These can be inserted into the human body without being too intrusive, and can release both radiation and chemicals at predetermined times or constant rates, depending upon what is necessary. This would have huge implications for patients, for example, patients needing chemotherapy could do it themselves at home, without the aid of a ridiculous amount of machinery. I was stunned by the progress being made, especially since our lecturer said these could be in place for everyday use by 2025.

it was pretty next level

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Oh Rochester
A patient's MRN is their eight digit identifying number. These were used back when Rochester was the location of the only Mayo Clinic. However, when Mayo expanded to places such as Arizona, the Rochester people decided they should tack an extra number at the end of every MRN, to be called the "check number", due to the staggering number of new patients Mayo was treating. However, the first number of every MRN was and still is 0. Christine and I wondered why they didn't just decide to use that seemingly useless number. After heated debate, we came to the conclusion that the entire Rochester branch was probably just stupid. Yep.

Unrelated, but one of our lab members has been to Rochester several times, and
he told me weather horror stories today. XD

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Drone
Apparently we now have a drone? That's what I've been told anyway. I have no idea why we need it, but apparently, a few people were taking pictures with it in a small conference room or something. Isn't it dangerous to operate those things in cramped places? Oh well, all I know is, I wanna take it for a test spin. ;)

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Seniority
So we got a new guy in our lab this week! Since the badges for new employees always take a few weeks to print off, every time he wants to get into a place requiring badge clearance, I should go with him because I have a badge. Dang, I feel important.

Week 7: New Responsibilities, New Antics

I walked into the clinic, ready to start a new week.

I take the elevator two stories underground, to the Lower Level.

I proceed to trip on a chair in my haste to make it to the lab. (Don't ask me how that's possible.)

So I got some new jobs to faff around with this week. Let's talk about some of the more interesting ones.

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Hardcore Debugging

Remember when I used OsiriX to blur out patient information on CT's and ultrasounds? OsiriX is essentially a local platform upon which one may view images, and it has a web equivalent in ResMD. ResMD has many key advantages over OsiriX, mostly stemming from its connection to the internet. I was introduced the software in more or less the following way:

Christine: "This software has more bugs than a trashcan full of rotten fruit in the Amazon, and we need you to uncover them all."

Me: "I...see."

Christine: "So basically, try to break the app. Go crazy. Do whatever you want. Just make sure you write it down."

Me: "Sweet." Breaking things. Now THERE's something I'm good at hehe

I'm pretty sure I crashed ResMD at least 10 times, and no that's not an exaggeration. I then emailed out my page-long report of errors I came across, but to spare you from reading that, I'll abridge it for you.

'mhm yeah uh this is trash please fix k thanks bye'

It didn't help that I was running it on Internet Explorer (Chrome wasn't on the desktop for whatever reason), due to which I'm sure there were some compatibility issues somewhere. But maybe that's just me.

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Liver Lottery

Another job I was tasked with was to find livers with the more quantitative information surrounding them. That probably made no sense, so let me explain.

The fields of radiology and pathology are quite interconnected. At Mayo Clinic, both departments often end up treating/diagnosing the same patient livers for different reasons. Our radiology department wanted to know how accurate our diagnoses were, so I was given access to a report database called Illuminate Insight and told to find liver reports from the pathology department that had a ton of numbers in them, so that our doctors could cross reference radiology reports to check for accuracy. Accuracy seems to be a common theme surrounding the work I do.

In any case, I learnt a lot of new medical terms, but from steatosis to Reye's syndrome, none of them boded well for the patient. :/

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So I Guess These Lecture Stories Are A Weekly Thing Now Eh?

The lecture I attended this week discussed the flaws in the RECIST form of tumor measurement, quite a similar topic to my research question, though I'm focused more on the data collected, rather than the actual measurement process.

To elaborate, imagine a pool like the one pictured below:

fancy

The RECIST method of measuring lesion volume would take the longest (or, depending upon the situation, shortest) 'line' on one side of the pool and multiply it by both an estimated depth and the longest 'line' on the other side. Quite an inaccurate way to go about things. 

What was proposed was to inject a harmless but easily scannable chemical into a lesion and let it diffuse, before using a certain software to calculate the volume, extremely accurately might I add.

At one point early in the talk, the lecturer asked us to use RECIST to measure a pool pictured on a screen, so we could compare it to the actual volume. The dimensions were 62 by 20 by 5. I thought to myself 6200 square feet, and waited. He kept prompting us to answer, but eventually gave up and said 6000 square feet.

Me: Um..."

Host: "Yes?"

Me: "6200, actually."

Host: "Ah. Right."

ikr

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Grant Granted

Remember when I said the CORE lab could be receiving a grant a few weeks back? Well, it seems there's an overwhelming chance we'll get it. Score!

Eyyyyy

See all you fantastic people next week. Ciao!

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.