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!

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

Hello!

If you're reading this, you likely have some level of interest in my Senior Research Project or the SRP's as a whole. In which case, welcome! Stick around, and let's see what we can learn.

My name is Pranav Suresh, and I'm a high school senior attending BASIS Scottsdale. As part of graduating with high honors as a senior, I have to complete a Senior Research Project entailing a lot of research (as the name suggests), and a presentation at the end. I personally am interning with Dr. Hara at the Mayo Clinic. Eventfulness and knowledge will be had :D

The clinical trial method of analyzing lesions and tracking their progress is the most common method used throughout the world, and at Mayo Clinic as well. The core lab method is the new method Mayo clinic is proposing. My job is to help find which approach has more success. For more details, check out my blog post titled "Senior Research Project Proposal".

In any case, I'll be sure to keep you posted on what's going on.