A Retiree & New Beginnings

Hey readers,

I write to you with a heavy heart... our team lost twice in the final round at the AZ Regional Science Bowl competition and earned 2nd place. After staying undefeated for the entirety of the tournament, we came up short against BASIS Mesa Team 1. We had a fun time and put in our best effort, but it's hard not to have regrets and wish certain questions went differently. Since we didn't move on to Nationals, my Science Bowl career is officially over -- what a wild 8 years it has been! So, in a final ode to Science Bowl, I wanted to thank all my teammates from this year and past years... I wouldn't be here today without you guys.

Yash-ip out... MUB MUB. :(

Ok... now back to my project. This next week is the final week officially at school for seniors, so we have reached the home-stretch for the Literature Review and Methods sections of the paper. I have been editing extremely carefully to clarify and trim all parts of my paper (entered the weekend with more clarifying than trimming, as I am now 800 words over the 3000 advised word limit). But, that's part of the grind. I will start by fixing the rest of my methods section, including adding the following figure to clearly display my samples more clearly and perhaps save some words.

Here's how I was thinking of showing my samples... let me know what you think!

My plan is to rewrite each section from start to finish today, so I can fix any other errors and remove extra words.

Regarding data collection, I have finished the simulation part of my experiments with the Rutherford Universal Manipulation Program (RUMP). RUMP is a really powerful program, as you can simulate the RBS spectra (basically the elemental composition that you receive) for various samples made up of layers. For instance, I can input a layer of blood (which is just the relative composition of blood's elements, so they sum up to 1) above a layer of Silicon or a microscope slide. Then, with a plot command, I can see what theory predicts our spectra should look like. I can then anticipate what sort of results we may get. However, the most insight often comes from comparing the theoretical prediction from the simulation with the experimental results. These are the reasons why I think it is definitely worth taking the time to simulate before we take our bulk measurements.

This week, I plan to finish analyzing and discussing the findings from my simulations with Dr. Herbots and finalize my Lit Review and Methods combination. Starting next week, since we have prepared all of the coating/substrate combinations, I should be on track to go into the lab 3 days per week and do the measurements with 3LCAA (to characterize the surface energy of the samples -- the A samples in the figure above) and then perform RBS on the blood samples (test uniformity with elemental composition -- the B samples). 

Such a strategy is slightly different than I originally planned, but as I stated last week, Dr. Herbots and I determined that doing many measurements at one time would be more feasible and introduce fewer confounding variables than taking lots of data over time. 

The data collection will be in 2 stages: (1) 3LCAA from Feb 5 - Feb 9 and (2) RBS from Feb 9 - Feb 19. This should be enough time to finish data collection by February 20th, as initially planned. 

Well, it's been a wild week, but that's going to be the norm from now on... I'm really excited to put my best product out there for the Lit Review/Methods and finally get back into the lab! 

Cheers,

Yash

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"Where Ya At" - Future

"Your paper should be less comp bio and more co-biolog." When these words -- I like to call them revolutionary -- were uttered from Max's mouth with his trademark wink and smile, the other four of us in our group stared at each other in silence for a few seconds before we all cracked up.

Max is the Kanye of AP Research

This anecdote pretty much sums up our group's feedback from last week; we all got some amazing feedback (in the above case, Divya was told to connect her research to the biological implications more) and had fun doing it. The critiques were really helpful, as I got a chance to look at my mistakes and the mistakes of others critically and carefully, and our group's discussions were a really good break from solely working on my project (jk. never... too much HemaDrop = ain't enough HemaDrop). 

After meeting with Mrs. Haag, I'm refreshed, prepared, and ready to revamp my lit review and methods combo package. In case you were wondering, some issues I was encountering were detached claims from justifications, lack of credibility descriptions, and a bit of unclear/esoteric parts of both. I will be submitting both in the next 2 weeks.

Since my project involves wet-lab work, I have already begun implementing my methods. I have prepared the coatings of various dilutions, acquired the necessary substrates, and made the pairs of identical samples (one for characterization with 3LCAA, one for blood analysis). I've been really fortunate to be able to get a head-start on this step, so I am excited about that!

I'm as happy as Drizzy (featured in this blog in honor of our OChem rap video)

However, I am slightly "behind" on analyzing the samples with 3LCAA and RBS because I idealized the process in my schedule slightly and I am waiting on some safety forms at ASU. I have a specific plan for making these up, with the logic that I can perform all the analysis from 3LCAA and RBS in longer session rather than 1 sample at a time. This way, I can standardize my results by limiting potential confounding variables from doing tests and different days, and it is more convenient once I have the apparatus set up on one day. So, rather than measuring a few samples each day, once the third trimester starts, we can perform the experiments in larger chunks, which is nice. Additionally, I can prepare the apparatuses and try to prevent major obstacles for the days until then (including preparing the samples, etc.).

On the point of preparation, Dr. Herbots has always emphasized to me the importance of preparation before conducting an experiment, so I am excited to add that I have been conducting simulations as a way of preparing for the results I will get and establishing what theory predicts the results should be. By doing these simulations on a program called RUMP (Rutherford Universal Manipulation Program -- a program made in the 1980s with FORTRAN), I am preparing myself for the results and will have a good comparison for the experimental data.

Example RBS spectra from RUMP

So far so good, except for the change in schedule, which made it easier and more feasible. The simulations have been taking up a lot of my time,for a journal paper, so I'm excited to present that data in my project too, since I think it's really interesting to compare simulations to data from the lab (and write up some preliminary results)! So, that's where I'm at...

I'm really excited to start working in the lab 3 times per week and getting some results! Thank you so much to Mr.s Haag, Rema, Kimy, Max, and Divya for helping me edit my methods and literature review.

Here's to another week of great research (IMPLEMENTATION)!

Cheers,
Yash

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We're Back! And Reflecting on My Methods

Hey readers!

Phew... it feels so good to be back. After over 1 month without blogging, we are now going to be consistently blogging every week as school comes to a close (!?), and we all go our separate ways to implement our methods.

Senior year encapsulated with a meme...

Right now, we have submitted a working version of the methods section that will appear in our final papers. Now, our job for last week and the next week was to divide up into groups and fix our mistakes (they were plentiful, but it's all part of the process).

Although I will be receiving feedback from my group on this upcoming Wednesday, I think writing about what I perceived as strong and weak in my methods beforehand will allow me to critique my own methods from the lessons I learned last week and go into the feedback session with the methods fresh in my mind. So without further ado... let's do this!

The first weakness of my methods is the limited credibility that I used. This limitation was a by-product of my methods section exceeding the word limit of 1,000 words; the places where I tried to cut was the credibility because many sources overlap from my literature review. However, from going over other methods and doing a bit of introspection, I realize that some parts of my methods section are not supported fully. I need to fix this by explaining the methodology of the source and expanding upon the credibility of the authors.

In order to do this, I will have to fix another weakness of my methods: its length. I am 587 words over the word limit. I think the best spot to cut words is towards the beginning when I explain the type of method I chose. Although I tried to make this part extremely clear, it could be shortened. In my group editing session, I will also try to ask for spots that are unclear, as this often correlates with verbosity. One potential way for me to shorten my methods would be to insert my sample matrix as a table instead of describing it in so much detail (so the reader can see it). Max had a similar situation with this instructions. Just a thought?

Finally, I would like to explain some of the technical terms in my methods in more detail and more thoroughly because I feel that they were slightly esoteric (major L) at some points. These include the concepts of 3LCAA and Rutherford Backscattering and the qualitative markers of dis-uniformity.

These weaknesses sum up the general trend of my methods -- needing to say more in less space. However, I am confident that with the help of my group and by looking over my methods even more carefully, I should be able to mitigate these problems. Another solution would involve chopping 200 words or so from my literature review, so my word count is still on track. I am very happy with the level of detail I could provide about my method including the various validity and ethical precautions (except I forgot to talk about the course -- RIP).

Identifying these weaknesses is the first step, and by working on my methods with my group, I am confident that I can make my methods more concise, more understandable, and better!

We are optimistic on this blog, and for good reason!

Here's to another great week --  I will keep y'all updated on my progress on my methods and implementing my research! 

Talk to you next week (for real)!

Cheers,

Yash

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P.S. I tried to experiment with the formatting/layout (doesn't deserve to be called an aesthetic) of my blog. Let me know if you think it looks worse or better!

Smooth Like Cocoa Butter

Hey readers!

This week, we turned in our methods proposals for IRB approval to the sweet smell of cocoa butter (If you don't smell like success, how can you be successful??).

This blog is, in fact, special cloth talk.

I was able to write out the research design for my experiment, which is a mixed (quantitative and qualitative elements), prospective study. As I wrote about controls, confounding variables, and ethical precautions, I felt like a real researcher (which is, I guess, the point of this class). It's pretty cool stuff!

Wish me luck for getting approval!

Now, I have a plan for how to conduct my research, and by next week, I will even have my methods section done. I'm on top of the world!

I am Roy Williams.

But, wait. The hard part is coming up soon -- implementing the research. You know what they say: don't count your data before they hatch!

Congratulations... you played yourself.

Since I am employing mixed methods for a lot of sample combinations, I am going to start data collection in the lab before the 3rd trimester, so I'll start on December 26th (Happy Holidays?). Since I have to finish obtaining results by the middle of February, I will finish by February 20th. After that, I will need to finish analyzing my results and write up the results/discussion section and the conclusion. After all, final presentations are May 17th!

As DJ Khaled would say, "they" don't want us to plan our implementation out, so we got to plan our implementation out!

Here's my detailed plan for implementing my methods:

Week	Tasks
1 (Dec 26 - Jan 1)	prepare substrates and coatings (all compositions and dilutions),  apply coatings to samples to make 12 pairs of identical samples (1a - 12b),  label the samples and create master spreadsheet,  obtain consent from participant (and his parents),  preparing 3LCAA apparatus
2 (Jan 2 - Jan 8)	perform 3LCAA on samples 1a - 12a,  finish data analysis of 1a - 6a for 3LCAA images using Inkscape
3 (Jan 9 - Jan 15)	finish data analysis for 7a - 12a for 3LCAA images using Inkscape,  extract blood and apply it to samples 1b - 3b,  perform RBS on samples 1b -3b,  finish code sheets for samples 1b-3b
4 (Jan 16 - Jan 22)	input final surface energy values into the master spreadsheet,  analyze RBS results for 1b -3b,  extract blood and apply it to samples 4b - 6b,  perform RBS on 4b - 6b,  finish code sheets for 4b -6b
5 (Jan 23 - Jan 29)	analyze RBS results for 4b -6b,  extract blood and apply it to samples 7b - 9b,   perform RBS on 7b - 9b,  finish code sheets for 7b -9b
6 (Jan 30 - Feb 5)	analyze RBS results for 7b -9b,  extract blood and apply it to samples 10b - 12b,   perform RBS on 10b - 12b,  finish code sheets for 10b -12b
7 (Feb 6 - Feb 12)	analyze RBS results for 10b -12b,  compile quantitative measurements of uniformity for each sample,  review qualitative coding sheets to establish gradation and create the scale
8 (Feb 13 - Feb 19)	TBD -- room in implementation for unforeseen delays or obstacles.  or I finish implementation 1 week earlier, and can start writing up my results.

My implementation will be very iterative, since I want to treat all my samples identically. One benefit of this approach is that if I am ever running behind, I can make up time by simply spending more time in the lab to run more samples. The analysis of my data will involve finding the average difference in composition for elements like C, N, O, Ca, K, and Fe for 2 different spots on a sample (using absolute value of course to prevent cancelations). This will be the quantitative measure of uniformity. I will put this in a table with sample type, surface energy, and the quantitative measure of uniformity shown. Additionally, the qualitative data will rank each sample relatively compared to other samples in terms of cracking, cratering, phase separation, and moisture. The combination of quantitative and qualitative will let me characterize each sample. Additionally, example RBS spectra can be shown for individual samples in order to demonstrate that elemental composition can be found with HemaDrop analysis.

In mid-February, I will start writing up my results and discussion. In this way, I can have a final draft of my results by March 4 and edit tirelessly for a final research paper by March 20. By the end of April, I can have a polished presentation!

Sorry for the slightly late post...

Let's secure the bag this week in research, and keep wearing that cocoa butter, so everything goes smooth!

Cheers,

YP

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Elevating the Elevator Pitch

Hey readers!

This week, I worked on my Methods Proposal. For my blog post, we were given the task of making an elevator pitch!

Here is the video from YouTube. Hope you enjoy!

Let's have another great week of research!

Cheers,

YP

The Methods to My Madness

Hey readers!

It's been a productive few days -- here's what I've been up to! This past week, I've been working on my Methods Assignment, where we were given the task of honing in on the methods of 4 (I did 5) sources, examining their methods, and applying their findings to my initial idea of my methods. Since I turned it in yesterday, here's what some exciting new information I found.

Dab, Squidward...Dab!

Although going into this project, I definitely knew I'd need a quantitative method to perform tests to optimize the HemaDrop preparation method to create uniform thin solid films of blood. I was like Squidward in this parade: I knew what I wanted to do (dab, aka develop a solid experimental design), but I need some instigation.

Nonetheless, studying the methods of others allowed me to determine specifically the type of experimental procedure I want to conduct. Additionally, sources, like Acharya et al and Dar et al, emphasized the importance of using controls in experimental studies. In this way, I can prove causation from the results from using hyper-hydrophilic films by manipulating variables in a controlled manner.

Triggered...

Additionally, the important aspect of all procedures was the emphasis on consistent, reproducible sample preparation. For this, I definitely need to establish a clear protocol for sample preparation. Another aspect I realized about my methods was that to check sample variability, more participants should be used than just me. In this way, I can greatly increase the validity of my study. To get these participants, I will need to adapt our current IRB approval and consent forms to apply directly to my project. I feel good about this, as I was part of the IRB approval process at ASU, so I have some level of experience. The laboratories we work at are already Biosafety Level 2, which is required for obtaining human blood samples. In this way, my research will also be ethical. I will most likely use fellow interns as participants (convenience sampling), as they will be willing to be pricked (even though it's painless) and at the lab anyways.

That's me crossing over my methods section and nailing the 3-pointer.

An unexpected part of my methods that I uncovered with the methods assignment was that I definitely want to incorporate qualitative observations into my methods. As seen in Acharya's thesis, specific criteria like phase separation, cracking, cratering, and lack of uniformity can be used to classify samples and explain quantitative results. This will really give my research a holistic perspective that would otherwise be lacking.

I also realized that our procedure for capillary sampling can be much more streamlined. Although we did use the correct grade lancet for pricking finger tips, specific procedures, like those outlined in Fan et al, which employ rubefacients (dilate the capillaries) and capillary tubes, increase the validity of the results, as those are the standard of care for obtaining microliters of blood from patients.

Capillary sampling in action!

By following a more standardized procedure, our results can be more standardized and replicable.

Now... what am I worried about?? 

Rip...

A major concern that I have with my research right now is making sure I have enough time to collect data and perform all my experiments within a few weeks. I'm trying to fix this by planning out a clear schedule with Dr. Herbots and getting ahead on testing by starting in January (probably). By next week, I should have a clear picture of my research plan and get a headstart on my proposal!

Well, in the meantime, let's keep loving blood and doing some fun research!

Cheers,
Yash

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Started from the Bottom, Now I'm Here...

Hey readers!

Wow, it's been way too long... more than a month! Since I last posted, so many things have changed (good and bad) -- my literature review has been finished, I submitted some college applications, the weather is nice now, and Donald Trump was elected president. Other things haven't -- the Cardinals suck, the mini-dab is still fashionable, and Ashwath's memes are dank as ever.

Before I get into the meat of my post, I'm super excited to announce that at the 2016 American Physical Society Fall Meeting at New Mexico State University, I presented the research we've done so far on HemaDrop™ and got an award for best undergraduate presentation. Here's the link to a video of my presentation! The reason I'm talking about this experience on my blog -- apart from trying to maximize the views on that video -- is that I think that AP Research, Mrs. Haag and Dr. Herbots's help, the comments from you guys, and my literature review allowed me to understand and articulate information about my project in a way I never could before. So, thanks for that!

That's me getting the certificate and cash from Dr. Zaniewski!

Now, I'm going to talk about how far I've come, where I'm at, and what I have to do. First off, I think I've come a long way from the beginning of the year. Even though it may seem like I had an idea and project from the get-go, I have grown to embrace what I originally feared -- the actual mechanisms of creating a hyper-hydrophilic film. Before, the complexities of surface-energy coatings and substrate smoothness made me a nervous, but since that was where my research gap is, now I am all about those 2 topics. Additionally, I learned much more about the implications of my research and the importance of microliter blood analysis. Although I knew vaguely about anemia, I never understood the nuances of hospital-acquired anemia that I found through the conversation between sources like Thakkar et al, van der Bom et al, and Salisbury et al. Moreover, explaining my project to Mrs. Haag and writing it all out helped me think about HemaDrop in a completely different way, with greater connections between disparate parts like blood properties, hyper-hydrophilic films, and blood testing.

Right now, I've finished my literature review and started embarking on figuring out my methods. My job for the next trimester is to figure out how I want to answer my question and conduct my experiments. Although I know my methods will be quantitative, there are some qualitative aspects for describing samples, which I definitely want to have as part of my results. Additionally, I need to see how studies in the past have conducted testing with many different types of samples and analysis methods efficiently (trying all combinations in the best way to maximize information). Finally, I need to examine different analysis techniques (e.g., atomic force microscopy, three-liquid contact angle analysis, terahertz spectroscopy, RBS, and PIXE) and justify which ones are best to use for the data I want to collect.

Here's to more fun times in AP Research!

Cheers,
YP

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