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.

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.

---
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

---

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.

---

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.

---

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!

Week 2: Computer Shenanigans and Cool Software Ahoy

NOTE: I copy-pasted this post into blogger and then posted. Apparently, that makes the words cut off and finish on the next line making the entire post look disgusting. Additionally, I can't individually change each cut-off word by pressing enter before the word, because each time I press enter, more lines get messed up. So, this post looks bad but future ones won't, I promise! Thanks for bearing with it.

First week complete! Fun stuff. Sorry about the delay in the 
expected date of my update.

Monday

As soon as I walked in I was flooded with more papers and 
contracts to sign (dang, I thought the 50 total forms I filled out previously 
were enough). Then, I had to log onto a computer and go through 
some online training videos followed by little quizzes. Little did I 
know that the greatest challenge in my internship would come so early on. No, not the training videos and quizzes. Logging onto a Mayo Clinic computer. 

9:00 AM

Attempts to log on have failed. Clearly, there is an issue with my credentials. My supervisor and I decide to call the Mayo helpline to patch us over to the appropriate person to assist us. 

10:00 AM 

After having heard "can you please hold" at least 5 times, we finally got someone to send us a link to reset our password. Unfortunately, that link redirected us to the Mayo homepage. My supervisor comments on the amateurish build of the Mayo Clinic employee website.

11:00 AM

I had lunch. Salmon. It was good. 

11:30 AM

After sending all the appropriate individuals an email from my online Mayo email account (which I had to access through a personal laptop) regarding my password situation, I get an email back from one person saying that it could be possible my Mayo email is deactivated, thus meaning my Mayo computer logon credentials were also deactivated at the moment. I replied that since “I sent an email to you through my Mayo email address, my email address must surely be activated.” My supervisor comments on the stunning intelligence of the human race.

12:00 AM 

Since my initial logon requires my in my password the last few numbers of my social security number, my supervisor questions my ability to remember my SSN. I reassure her that I do indeed know it. 

12:30 AM

Success! It turns out, it was a fault in the system, not us. (Whew. I was beginning to doubt my ability to remember my social security number.)

Now is where the real fun begins. After breezing through the instructional videos, I had to make an Excel (Ah, Excel. Should’ve taken Mr. Mac’s term project.) spreadsheet that could easily compare values from lesions from the Core Lab and the Clinical Trials for the radiologists in the area. This way It’d be easier to determine which method was more accurately in data collection, and I’d be able to do something for my supervisors which they would be tasked with doing themselves had I not been there. After three tries, I finally produced something to everyone’s liking. 

Then, as the day was coming to a close, I was provided with a radiology research paper to peruse for an hour. It was graduate level. Hoo, boy. Let’s just say trying to understand it is like trying to understand Finnegan’s Wake. You don’t.

Tuesday

New day, new jobs.

I was assigned to catalog and organize different medical cases involving tumors and/or lesions logged in the AZ Mayo Network. It got somewhat repetitive, but I learned an Encyclopedia Britannica volume’s worth of general medical terms, at least it felt like it.

This time, I bought catfish from the Mayo Cafe for lunch. I've been having a thing for fish lately.

Later on there was a meeting between all the radiologists and officials in the vicinity to discuss top-secret matters. I happened to be in the room where the discussion took place, so naturally I crept into the shadows and eavesdropped. I’m pretty sure they knew I was there though. The reason I suspect these matters are top-secret is because I was told to stay put when the first meeting on Monday happened. If I hear anything groundbreaking, I’ll let you guys know. In any case, the conversation was tough to follow, but I had an easier time of it than I expected. Maybe that research paper I read yesterday subconsciously helped? 

And finally, I was given access to an enormous database of cluttered data and software such as MintLeaf to analyze it properly. I was told to log some sample data into my spreadsheet to see how effective it is. My supervisors told me they’d check out my work before I returned next Monday. Hopefully they think it was effective. I thought it was effective. ¯\_(ツ)_/¯ 

In any case, the work I’m doing is quite interesting from the start, and my three supervisors, Dr. Hara, Dr. Zwart, and Kelly, are awesome! I’ll be sure to have more stories to tell next time. See ya!

Week 1: Quick Update

Hello! This week I decided to take my week off, as we are permitted one week off during the duration of the Senior Research Project (SRP). I did this because, due to some complications, Mayo Clinic had told me that I could not start my internship until February 16.

But hey, that's tomorrow! I can't wait. Expect an update tomorrow or the day after on how my first few days went.

Senior Research Project Proposal

Pranav Suresh

Title of Project: The Accuracy of Tumor Identification

Date: 9 January 2014

Statement of Purpose: 

The SDTM (Study Data Tabulation Model) method of identifying tumors clinically and lesions is widely used throughout the globe, but an increasing number of scientists are finding minor problems with it, specifically with the methodology used. (Litzsinger, 2014)The actual scientific process and equipment used vary from hospital to hospital, however. The Mayo Clinic is experimenting with a new method, the core lab method, with the goal of increasing accuracy of tumor detection. The question is, does it surpass the clinical (old) method? My job will be to help analyze data from usage of both methods of analyzing data (confusing, am I right?) and determine which is better.

Background: 

I have no prior experience with lesions themselves, though my interest and study of biology and statistics should help. I am very interested in radiology as well, which will make this question quite interesting to research. I hope to expand both my biology and statistics knowledge from this project, specifically radiology and analysis of quantitative data. I will also hope to gain valuable internship experience, and to be able to help Dr. Hara and others where possible. If I am able to help the Mayo Clinic determine that this new method of detecting tumors is indeed more accurate, it will help patients in the future, and though I may not have been a big part in the research, I can still feel happy about it.

Prior Research: 

There is some context to be provided on how tumors and/or lesions are normally identified before analyzing the way it is done.

Tumor markers are markers that can be produced by both cancerous cells and immune cells in response to cancer cells, as stated by the American Cancer Association. (ACA, 2011) These markers are easier to detect than the cancer cells themselves, so many methods to diagnose tumors involve them. To increase the overall accuracy of diagnosis, this may be combined with other tests, such as biopsies. (CRU, 2009)

Tumor markers are measured by taking a sample of possibly tumorous tissue, or blood in the case of leukemia, and analyzing them of a period of days at a laboratory. If the patient has already been diagnosed with cancer, these markers can find whether treatment has been working or failing. (Litzsinger, 2014)

Examples of types of tumor markers are ALK, AFP, B2M, beta-hCG, BRAF, Mutation V600E, and many others. (Mayo, 2014) While these are not completely accurate, many hospitals and laboratories are doing research to find methods and markers with increased accuracy, such as in Mayo Clinic. For example some are using a new type of marker known plainly as biomarkers, which are in theory able to detect malign tumors earlier, thus limiting mortality from a possible cancer. (Crinion, 2012)

But this all remains constant. What really changes between the two methods is the analysis of numbers gathered from it. 

To start off, the clinical analysis uses multiple doctors over the course of several days as they become available. The core lab uses one person through the same period to increase accuracy, as different individuals may interpret data uniquely. The core lab also compares lesion progress to all previous records, rather than the clinical method, which compares only to the most recent record. In addition, the core lab has some parts of the data collection process automated, clearing human error in those areas.

Significance: 

It goes without saying that body-internal cancers kill many every year, and therefore the screening techniques for finding and subsequently destroying tumors must be as accurate as possible. If the accuracy of even one diagnosis is improved through an implementation, or lack thereof, of Mayo’s new core lab method for scanning for tumors, the internship will have been worth it to be a part of that. The core lab is merely an experimental add-on for the time being, but if successful, can become part of mainstream medical practice.

Description: 

I will be analyzing (compilation, comparison, and assessment, followed by a fully formulated hypothesis) data sets from tumor scans, in addition to doing minor work for doctors who need it. Depending upon the number of patients available, I will be comparing anywhere between 20 and 50 patients’ data over the course of 10 weeks. While my on-site mentor is Dr. Hara, I will be working with and helping a few others staff members as well. I will present my findings and a conclusion at the end of the year. 

Methodology: 

I would start by formulating a hypothesis regarding the two methods. Then, I would analyze data sets on a daily basis and alter my existing conclusion as appropriate. Finally, I would make a more lay-audience friendly PowerPoint and speech to explain my and the clinic’s findings and their implications. 

As for the data analysis specifically, I would, in addition to data sets from the standard method and the new method, need a control group of sorts, showcasing the base values for each quantity in a data set for a tumor. Variables would include, but are not limited to: doctor, disease, lesion/tumor size, lesion/tumor number, etc.) On a weekly basis, I would need to compare all three data sets and their effectiveness. Results will be compiled to form a conclusion at the end of the internship.

Mayo Clinic has informed me that I will be given access to the clinical database for lesions and tumors. Using it, I can make charts for both the clinical method and the core lab. 

Problems: 

I don’t know anything about radiology specifically, so I will have to research the background behind the field in order to understand my role in Mayo Clinic’s experimental approach. In addition, I will need to find a way to summarize medical data into a meaningful conclusion that anyone will be able to grasp. I will also need to dress professionally being an intern and all. (Something I’ve had a problem with - and by that I mean I always forget - for a long time.)

Bibliography: 

Study Data Tabulation Model (SDTM). (2014, November 30). Retrieved December 10, 2014, from http://www.cdisc.org/sdtm

Cancer screening. (n.d.). Retrieved December 18, 2014, from http://en.wikipedia.org/wiki/Cancer_screening

How is cancer detected? (2009, November 16). Retrieved December 18, 2014, from http://www.cancerresearchuk.org/cancer-info/cancerandresearch/all-about-cancer/what-is-cancer/detecting-cancer/detectingcancer

Tumor Markers. (2011, December 7). Retrieved December 18, 2014, from http://www.cancer.gov/cancertopics/factsheet/detection/tumor-markers

Cancer. (2014, February 22). Retrieved December 18, 2014, from http://www.mayoclinic.org/diseases-conditions/cancer/in-depth/cancer-diagnosis/art-20046459

Can brain and spinal cord tumors in adults be found early? (2014, March 5). Retrieved December 18, 2014, from http://www.cancer.org/cancer/braincnstumorsinadults/detailedguide/brain-and-spinal-cord-tumors-in-adults-detection

Kenny, S., & Litzsinger, M. (n.d.). Strategies for Implementing SDTM and ADaM Standards. Retrieved December 18, 2014, from http://www.pharmasug.org/2005/FC03.pdf http://www.pharmasug.org/2005/FC03.pdf

(n.d.). Retrieved December 18, 2014, from http://pathmicro.med.sc.edu/mobile/m.immuno-18.html

Radiology. (n.d.). Retrieved December 18, 2014, from http://en.wikipedia.org/wiki/Radiology

Interventional Treatments for Liver Disease. (n.d.). Retrieved December 18, 2014, from http://www.sirweb.org/patients/liver-disease/  (Not entirely related but still provided context for me.)

Crinion, J. (2012, January 1). Download PDFs. Retrieved January 11, 2015, from http://www.sciencedirect.com/science/article/pii/S1053811912007732