Progress: Sample Preparation, 3LCAA, and More!

Hey readers!

What a week... we are in the home-stretch of data collection! Last week, I went in the lab on Tuesday, Thursday, Friday, and all day Saturday (anything to get the data we need on time!). But, of course, my amazing readers don't care about the time I spent -- you care about what I actually did and what goals I accomplished.

So, as you may know, the goal of my project is to optimize HemaDrop™ by finding the ideal combination of coating and substrate (to create the optimal level of hydrophilicity) upon which to solidify blood drops uniformly, quickly, and cost-effectively into a film.

To do this, there are basically 3 main stages of work in the lab for me:

1. preparing samples, 
2. characterizing the surface energy of each of the samples to quantify hydrophilicity with 3 Liquid Contact Angle Analysis, and 
3. testing the uniformity of the sample quantitatively with Rutherford Backscattering Spectrometry and qualitatively with observations. 

Due to technical difficulties (the fridge becoming a freezer and freezing all of our coatings -- there was literally snow in the lab), I started this week behind schedule -- our work in preparing the coatings the week before was worthless. So, on Tuesday, I re-made the secret sauce (aka, proprietary coatings) and prepared the substrates (microscope slides and Si wafers) for application. 

Dr. Herbots said that two of the coatings looked like beer, so I posed like this... it was wild.

One big change that we decided to make was to only use 1 type of microscope slide (borosilicate -- they're so accessible that you can actually buy them on Amazon and get them in 2 days #PRIME). The reason for this reduction in number of substrates was that the soda lime slides were not pre-cleaned and not sterile. Using these slides would introduce a great deal of error and even potentially compromise our other samples. 

But, don't worry, we won't be reducing the number samples... we're actually testing another coating with a different type of metallic nanoparticle (I can't reveal the identity in this blog unfortunately, but I think I can in my research paper), so now we have 2 substrates (microscope slide and Si wafer) and 5 coating treatments (no coating, metal 1 at high concentration, metal 1 at low concentration, metal 2 at high concentration, and metal 2 at low concentration). 

So, for all of you counting (I try not to nowadays...) that's 10 different possible combinations, with 2 of each combination being made (1 for characterization with 3LCAA and 1 for blood application) -- so 20 samples! We actually made 3 of each individual slides as a validity precaution to make sure the coating was applied correctly to at least 1, so that's 60 samples, but we will only end up using 20, so don't even worry about those for now.

For 3LCAA, we went in on Saturday ready to perform some measurements, but ants had attacked our store of alpha-bromonaphthalene (a mouthful which is the hydrophobic liquid that happens to be the poison used in ant traps, so ants love it unfortunately for them and my schedule).

In this meme, the most interesting man in the world represents the most interesting hydrophobic liquid in the world!
Also, I didn't bother removing the beer from the meme, because I figured we could just call that coating ;)

Additionally, the samples are extremely hydrophilic, so when we apply the DI water drops to measure the contact angle, the water is spreading out and wetting the samples. So, we devised a plan to reverse the usual order and start with alpha-bromo and then apply the water, so the samples would not be ruined from the first liquid (water) spreading out. We'll see how that goes -- worst case-scenario, we just use each of the 3 of identical samples we have.

So, after a few hours of purging the clean room in which we perform the 3LCAA of ants, we decided instead to perform 3LCAA all day on Monday (tomorrow) and work on making sure our samples were prepared well and ready for analysis. The samples are now sitting in the laminar flow hood in this apparatus:

We mac-gyvered a sample drying rack from sterile pipettes and aluminum foil, in a minor engineering feat!

I am confident that we can finish the 3LCAA characterization by tomorrow and (LATEST) Tuesday. Then, the plan will be to, in conjunction, start applying blood on the samples Monday, Tuesday, and Wednesday (and recording qualitative observations with my updated coding sheet). Then, on Friday RBS can be performed on a majority of the samples...

However, I see data collection with RBS taking 2 or 3 sessions, so I think that my data collection could spill into the week following the February 19th deadline (probably Wednesday). I understand that this is not ideal, but since I will have all the 3LCAA and qualitative observations finished along with most of the RBS performed by the 19th, I can definitely work on data analysis in that period as we fill in any data not collected yet.

I am working as hard as I can, and I would embrace working in the lab most days and analyzing data at home in the evening. Anything for the data! Moreover, I can write my results with a few blanks for data if I have to. My meeting with Mrs. Haag is on Thursday (3/2) rather than Tuesday the week that the Results are due, so that could also potentially give me a few days to write it up.

Sorry for the extremely long and slightly serious post, but I wanted to give you guys some specifics on my progress and plan for the next 2 weeks.

Although this week was intense, it is definitely exhilarating to be in the lab working on an experiment I designed, so that's awesome. 

On a personal note, I have exercised for 7 days straight, so hopefully I can keep that up too! 

Cheers,

Yash

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P.S. Thanks so much to Grady Day and Alex Brimhall for helping me out on Saturday... I can always use the extra hands!

Working Overtime

Hey readers,

The first weekend into Trimester 3 -- it's been a wild ride. Let's start off with the Super Bowl -- yeah, I wanted the Falcons to win, and just after I snapped everyone a picture saying it's over and rejoicing at the fall of the heinous Patriot villains, the Falcons's secondary crumbled. Matty Ice turned stone cold.

At least the memes are still dank as ever...

But, hey, at least I am not a sore loser (except...just ask Kimy and Divya).

Since the Super Bowl went into overtime for the first time ever, the theme this week is OVERTIME!

After I submitted my lit review/methods combo to Mrs. Haag on Thursday, this weekend I worked on a paper with Dr. Herbots for Biointerphases journal, lit up the dance floor at Sadie's (except not at all), and finished analyzing the simulations from RUMP. The RUMP analysis actually serves two purposes, as it is part of the data for our paper and helps me plan for my experiments/data analysis in the next two weeks.

I did it though, Dwight... I did it!

Right now, I am feeling super motivated to work on and finish my data collection especially since the nature of my research (collecting data at an actual laboratory) makes it easy to fall behind and hard to catch up. Because of this my biggest struggle will be to stay ahead of schedule and communicate very effectively with Dr. Herbots. Undoubtedly, we will face some obstacles (e.g., particle accelerator down for a day, contaminated sample, etc.), but having a flexible schedule and working as much as possible to get the research done should help me face them head on.

Like Tom Brady dancing...

My primary objectives while getting my research done is to balance the interests of the lab with the time constraints of my research project and get the best help from Dr. Herbots. My weekly meetings with Mrs. Haag (Tuesday mornings are lit) should maintain the urgency to collect data in the lab and not get sucked into other experiments or projects at ASU. Moreover, working closely with Dr. Herbots will ensure my research is rigorous and up-to-par. Not trying to suck up, but I am definitely super lucky to have both of them as amazing mentors.

I am super super excited to get some concentrated work done in the lab without having to go after school, so I do not see laziness as being an issue. After all, it's more time with the HemaBaes... 

So, overall I see complications with the lab equipment/scheduling as being potential pitfalls, and staying on top of my schedule and communicating very actively with Dr. Herbots and Mrs. Haag will make sure I can maximize the time I spend in the lab, so I can start data analysis as soon as possible. Performing the simulations before the RBS, as we have, also will give us a great starting point for our experiments. Also, having the pairs of samples prepared already gives me a great head-start for our bulk measurements of surface energy and RBS. There will be a lot of repeat measurements, so once we get rolling, collecting the data will come in bursts. And, if anything happens, I'm not afraid to work OVERTIME (looking at you, Atlanta)!

Apparently, pitfall memes are a thing in Pokemon? Well, we're not falling for it!

By avoiding these pitfalls, I should be on track to finish collecting data by February 20th, with 1 week for data analysis. I can also analyze data as we get it to speed up the process (e.g., 3LCAA images of slides to measure surface energy). Now that we have the samples prepared, the goal of this week will be to perform 3LCAA to get the surface energy of the samples (independent variable). Then, once this done, the uniformity test with elemental composition can be performed with RBS.

If you're wondering what else I've been up to, I have started taking some MIT OpenCourseWare classes for math and computer science to stay sharp. Also, my tutoring game is going strong. The goal for this week is to make it to the gym every day and work on my chess game too! 

I guess this applies to this blog, not Facebook...

Things are looking up! I will keep you guys updated about my progress this week. Tomorrow, I am going to the lab for the first time since I've been released from captivity (aka BASIS). But, Tuesday, I go back to meet with Mrs. Haag (jk...that is gonna be lit).

Signing off... cheers to another great week of research!

Yash

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P.S. Miss you, miss you! 

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