Sunday, March 12, 2017

RBS: Really Big Stuff

Hey readers!

It's been a crazy week, like always! Right now, we've basically finished the final experiment that I needed to have a complete set of data to answer my question. So, this week has been packed with 3 stages of research simultaneously: data collection, data analysis, and writing.

If you remember, at the beginning of my data collection stage, we were unable to do RBS (Rutherford Backscattering Spectrometry) on human blood. However, since performing RBS and determining elemental composition of 2 different spots is crucial, I still collected as much data as I could using Balanced Saline Solution (which mimics intraocular humor, so it's a complex ionic solution like blood). On Thursday, we had a marathon 10 hour continuous RBS session to take a bunch of data. RBS is super awesome, so even though this post is about my paper, I wanted to show you guys some really cool pictures of samples:

Here's the organization system I created for my samples  with a $1.50 box from Joann Fabrics!
Each compartment has a 8 mm x 8 mm sample wrapped in a cellulose wipe, to prevent contamination.
Here is a sample in the vacuum chamber on the sample holder.
The laser beam shows where the ion beam will hit the sample!
Do you see that purple light?
That is the sample (an insulator) fluorescing when the ion beam hits it.
Since Thursday, I've been working as hard as I can to finish analyzing this new data, with 46 runs of 100,000 counts (ions) each to analyze. I calibrated the energies, and now I am looking at the data to overlay spectra and calculate elemental composition (uniformity). It will be done by tonight.

The data has been extremely interesting so far, and I have a lot to add to my results/discussion section about it. We took the approach of finding the composition of a bare slide, a slide with coating, and a slide with coating and a saline drop applied. 

Check out this cool plot overlaying 100k to 400k ions hitting 2 drops on the same sample! The "steps" represent elements' compositions (e.g., K, Ca, Na, and Si)

Visually, we can see that the compositions are similar across 8 spectra, especially in the overlay.
But, don't worry, I have quantitative calculations of uniformity as well.
It's really liberating to have this data finally, as I have had the opportunity to analyze data continuously without waiting on anything. 

Now that we've talked about where I am on data collection/analysis and what I've been up to, let's hone in on the paper!

Actually it's due tonight...
Since I am still analyzing some data, some of my results sections and discussion sections still need to be written up, since I need to fill in some numbers and draw a few more conclusions from the new analysis I have been working on. However, they will be completed within the next few days, in time for my editing spot on Thursday. 

So far, I am really happy with the robust dataset I have collected. I have 3 parts of my results, including (i) 3LCAA data on the surface energy of my samples, (ii) qualitative image analysis of saline drops, (iii) Ion Beam Analysis of canine blood, human blood, and saline. I think that the amount of data and analysis I have done really answers my question and can lead my reader through logically why I decided to use this three-pronged approach. Of course, lots of data means I have a lot to talk about in all of my sections. 

Let's just say this isn't big data, but the data sure is BIG ;)
Apart from being happy with the data I collected, I think that the connection between my methods and results section is really strong, specifically how I describe my data analysis. When I edited my paper at the beginning of the first trimester, I focused on aligning these parts very well and connecting the importance of uniformity in a clinical setting to the data in my experiment.  


Now, for the weaknesses and what to look for... 

Always word count.
Since my paper is already above the word limit without the new data, I definitely need to figure out sections or parts that are dispensable. Anything that can be made shorter would be greatly appreciated.

Moreover, I think that something I really need to be strong are the transitions between the results sections and justifications of looking at specific samples. In the beginning of the project, I set ambitious goals and planned a huge experiment. However, we encountered some obstacles, so my actual experiment did collect a bit less data. Therefore, I want to make sure that as a reader, the justifications of only performing RBS on certain samples is robust enough (apart from the weak, hey, I couldn't). I think using the previous 3LCAA data as a way to narrow down and select specific samples to RBS was a solid approach though. 

The transitions better be good, but not too explicit either...
Next, I think that identifying any extraneous information in the Lit Review or Methods that doesn't perfectly align with the slightly modified experiments I performed would be a major key 🔑  in cutting down my paper.

Finally, I wanted to make sure that I connected my research to the applications clearly in the discussion (e.g., implementing HemaDrop as a technology), as that is ultimately the significance of my research and will make my project more focused and digestible for all.

I tried to break up the dense post with some dank memes, so hope you enjoyed!

Entering the homestretch, so let's goooo!
Yash 🦁

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9 comments:

  1. I think that your instinct about editing your paper is absolutely right. You had to change your experiment because of unforeseen circumstances; thus, you need to make sure your justifications are still as robust as your original plan. Furthermore, since your plan has changed, it's likely that not all things in your literature review currently align with your methods, as they ended up.

    They said you couldn't write a research paper, so you wrote a research paper. (sorry, that was so bad, and no one would ever tell such a RELATIVELY HEALTHY 17 YEAR OLD INDIAN MALE that he couldn't write a research paper)

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    1. This comment is so inspirational... This week was great, but we gotta persevere -- to make it to ANOTHA ONE!

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  2. Oh boy, that paper was long, but it was well done. The steaks were high this week, and you managed to pull through. I didn't have any major beef with this paper's overall argument. I'm sorry for all these udderly disappointing cow puns)/ Unlike your paper, I'll make this comment short and sweet (sorry for that zinger):

    Things I disliked:
    1. Too specific at certain points, when we don't even need the information
    2. Too vague at other points, and lacks enough information to give the reader a sense of what is going on
    3. Assumes the reader has a lot of knowledge (or maybe I'm just dumb)
    4. Wordy and confusing at times
    5. Did not provide context for microscope slide claim and Theranos example (please see my comments for more info).
    6. Way too long
    7. Too long
    8. Damn it, it was too long

    Things I liked:

    1. The figures and graphs
    2. Your examples that you use so that we mere plebeians can understand what you are saying
    3. How you show the clear need for your research
    4. How you show the academic gap

    This comment is very vague, but if you read through my edits and suggestions on your paper (which I put into a google doc. for you, so you're welcome) you will have a clearer understanding of what I was saying.

    Ok, that was a marathon, a looong marathon. You can see how much time it took me by looking at the time stamps on my comments. I start at 3:06 pm and end at 7:54 pm.

    Yash, in all seriousness, that paper was amazing. There are a few minor tweaks that you need. Please keep us peasants in mind when you're editing the paper. Overall, your research is incredible--and frankly--very significant. I applaud you and your hard work. Good luck bae.

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    1. ^^^I hope that comment doesn't go through one ear and out the udder ;) ^^^

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    2. ^^^You better stop drinking CALFine and hit the HAY, because its PASTURE bedtime^^^

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    3. Ok, that one did not make sense, so I'll just stop.

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    4. Hey Gursajan!

      First off, thank you so much for reading all of my paper and converting it into a Google Doc for editing. That was a big help! You really milked the cow puns for all they're worth...lol.

      When I reread my entire paper, I also realized just how long it is right now. Even though I transitioned between sections, I had been writing each section individually, so I am around 1,500 words over right now. I'll work on cutting some extraneous information, as both you and Ashwath said that I was needlessly specific in areas like the methods. Cutting down this extraneous information will allow me to expand upon my discussion section and explain concepts more concretely.

      I definitely agree that I need to be much more careful with my explanations and not assume knowledge. I was still trying to figure out myself what the results meant, so now that I have a first draft written, my plan is going to be to add as much explanation as possible for next week to increase readability.

      Thank you so so so much for spending your time on giving me feedback, both positive and negative -- you're the best!
      Yash bae

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  3. Hi Yash,
    Similarly to Gursajan, even though I said I wouldn't spend more than 2 hours on you, I ended up in my own marathon from 11:30am to 2 am. The trend of us taking forever to read your paper is a sign of a bad thing. If you turn this thing in right now either the reader didn't understand it and gave it a 0 or the reader didn't understand it and gave it a 100. Now we all want the reader to understand it, so here's my advice.

    The paper was absurdly specific in certain sections, we do not need to understand how each tool in your arsenal works. Simply talk about what their output means in the context of your paper. There is also assumed knowledge (not too much in the lit review) but in the methods it really showed. Several technical terms were explained in a very esoteric way, defeating the purpose of explaining them. But the thing is wayyy too long.

    But the your lit review did set up the paper for success, I clearly understand the purpose, the gap, and the significance. However, its the actual analysis holding the paper back. Revamp the explanations to focus on the average reader and you have a home run on your hands.
    -
    Ashwath V.

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    1. Yo Ashwath!

      I see you with the comments and on House Party ;) Thank you for spending your time giving feedback!

      I definitely do need to increase the readability of my paper -- both in terms of length and explanations. Like you said, I realized a lot of details are unnecessary for the paper in the methods. They'd be nice to have in a perfect world, but since we do have a word limit, I'd rather us that space to explain my results much more clearly and have people be able to read my discussion and understand it.

      I agree that lit review is the strongest part of my paper, and I need to work on connecting my methods and result back to that stronger foundation.

      Thanks so much for reading it!
      Yash

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