Steep Learning Curve

June 14, 2019

Azka Bukhari- Hogg Middle School: CS Educator

Prior Knowledge

The second week at Rice University’s PATHS-UP Research Experience for Teachers 2019-2020 has been quite eventful. I wanted to go ahead and summarize the extent of my research prior to starting the research. I googled the PATHS-UP RET page and found some interesting information. I tried to read the research on distancePPG; I understand that the whole concept of this project is to create a system of detecting vital signs in a non-invasive manner that is accessible to the under-served population. By reaching to teachers, the plan is to not only spread aware of STEM fields, but to educate, inform and encourage students about health in the under-served community.

Orientation & Yong’s Presentation

PATHS-UP team and Yong: our mentor

I presented my PPT early in the orientation and I met the rest of the team. Our mentor, Yong presented the research project that we would be working on- distancePPG.  PPG stands for photoplethysmography which is an optical method to measure cardiac-synchronous blood volume changes in face, finger and earlobe. In broad strokes, Yong explained the procedure of distancePPG and the various tools and libraries used by distance PPG and some of the challenges of using distancePPG. In layman’s term, distancePPG uses webcam monitoring while shining a light on a person- as the heart pumps bloods, the volume of blood in the arteries and capillaries change, this  leads to a small change in the skin color. DistancePPG measures this small change in skin color as the light shines on the person- some of the light reflect, some light is absorbed, the computer program calculates this light reflection.

Fig. 2

Fig. 2: Overall steps involved in distancePPG algorithm for estimating camera-based PPG.DistancePPG: Robust non-contact vital signs monitoring using a camera Biomed Opt Express. 2015 May 1;6(5):1565-1588.

Python is the programming language that will be used and two specific libraries that were mentioned were OpenCV and NumPy. OpenCV (Open Computer Vision) is a library of programming functions that focuses on real-life computer vision; it is FREE! This week I downloaded OpenCV and I have tried a YouTube tutorial (*tutorial link attached) – as basic introduction on how to use OpenCV with Python. NumPy, the other library mentioned, adds support for large, multi-dimensional arrays and matrices, along with high-level mathematical functions to open on these arrays. My experience with NumPy is minimal and I look forward to learning late next week. It was quite unclear how I am going to be doing my own research at the moment.

Scalable Health Labs & Reading

We visited the Scalable Health Lab to see the extent of their research. Mary Jin presented one of her projects that might potentially lead to detecting cancer cells without a biopsy. While, Anil Kumar Vadathya summarized his project as F.L.A.S.H- which stands for Family Level Assessment of on-Screen Time at Home. His project idea was to help reduce negative health impact of over-exposure to technology by monitoring the total number of hours children were watching TV. This was really interesting as this is quite close to our project when he broke down the process- the face detection and gaze detection.

As a group, we came together on Thursday and summarized what we read in the research paper. We went over the pseudo-code to understand how the program works. We weren’t sure about how well we did- but it was a starting point to tackle a huge task.

 

Learning Python

Christina introduced the team to edX, I started with the Absolute Beginners Course for learning Python. However, Pamela recommended codeHS.com, I picked this course because I can use this with my advanced classes and this is an excellent chance for me to experience it myself. This week, I have managed to get halfway through the Python course- I realized that I know a lot of fundamental concepts such as loops, conditionals and functions.

Screenshot of my CodeHS progress

Later in the week, Jimmy brought his own device that he created **. I have attached a picture of this experience- I will try this in my own classroom.  He decided to expose his students to a pulse oximeter that he purchased last year- this was followed by students creating their own pulse sensors using an Arduino and a pulse sensor bought from Amazon***.  Although, it would be replicating what Jimmy did, I think my middle school students would be blown away by the real-life application of Computer Science in the field of Health.

Walkaways

I am leaving this week- a lot more energized. I realized that being confused in part of the process of research. I am not used to feeling ‘lost’ and ‘confused’ being a teacher- this usually leads to PANIC! I have decided to use my confusion as a learning experience- when I am confused in Python, I realize that this is how some students might feel when they are learning code. When I listen to Yong’s presentation and Jimmy’s implementation, I learned that that it is my job as an educator to expose students to ‘very difficult’ concepts- things they might not grasp straight away. If we want our students to grow, we must give them challenging tasks. I have two ideas about where I would like to go with my own research project. First, I would like to create face detection and later- face recognition program. Jimmy has already done this, but I would like to try this myself. I can create a lesson with pseudo-code that I could use with my middle-schoolers. My second idea is quite interesting, but might not be do-able! I would like to see what would happen if the R.O.I was flashed with different colored lights- how would this affect the data being collected.

I’m still a little unsure about how my research project and poster will look like. I have seen some examples, but I am feeling a little anxious that I won’t do well. Shout out to Yong for breaking down tasks for us to do next week! Best thing this week! I really appreciate Professor Yong. d

*https://www.youtube.com/watch?v=YY9f-6u2Q_c

**https://learn.adafruit.com/make-it-pulse?view=all

***https://www.amazon.com/Asiawill-Pulsesensor-Sensor-Module-Arduino/dp/B00MB1LPUA?source=ps-sl-shoppingads-lpcontext&psc=1

Disaster In the Lab!

And the real side of research begins. After spending last week preparing samples we finally began running a crystallization experiment on Tuesday. It takes 48 for the induction time. Today when we went in to check the data my mentor declared the experiment a failure as dissipation and frequency should be inversely proportional but were coming up as proportional for some reason. Once we went to investigate  we discovered that the machine is leaking internally!!! So  needless to say my mentor is not happy and we are now spending the afternoon discussing with the tech at Qsense how to correct the problem. YAY science!

Weeks One and Two

It’s been a crazy week and a half.  Juan, my mentor, has shown me how to culture bacteria and mammalian cells.  We have then added flourscent dyes to use confocal microscopes to analyze different parts of these cells.  We have also worked on different dyes to get an understanding of what ultraviolet lights work of them.  I have reviewed the bacteria cell walls, organic chemistry,  mitosis and dna replication to get an idea of what is going on.  Still a lot to learn and beginning to do my experiments the next few weeks.

-Only the Beginning- Introduction to Instrumentation

One week down and only so many more to go!! I would have to say that my first week in Dr. Bruce’s lab was quite successful. In this week, I focused on the many lab instruments that will be utilized in my summer research. Some of these instrumentation’s  and techniques include: Aqueous surfactant preparation, sonication, and centrifugation. This week, I will become familiar with spectroscopy instrumentation and focus on measurements of fluorescence and absorption on Single-Walled Carbon Nanotubes.

 

 

First week summary

All is well in Dr. Gardea’s lab  as I learned how to run Zeta-potential analysis that tells us the potential difference between the medium and the layer coated around the nanoparticle, which tells us about its stability (the higher the number, the more stable the particle in solution).  However, we are having trouble getting graphs for the controls of TiO2, so we are adding different salts (KNO3 and NaCl) to help stabilize the nanoparticles and get better readings.

Labs are giving me life! :)

Hello my fellow science and math lovers. I am really enjoying taking care of my stem cells weekly. I have to change the media (solution cells are suspended in) daily so the stem cells can receive daily nutrients. If not, they will die. Today we pulled the stem cells from the liquid nitrogen and I was just so fascinated with this process. This is giving me a memorable experience.

 Thanks R.E.T!!!

Balling at the MEB

Meet MILFRED! Day one on the job and I was introduced to this amazing machine. Although a simple concept, ball milling has the potential to be extremely significant in the field of nanotechnology.

Down in material sciences, we are using the ball milling process to break apart weak bonds attaching layers of hexagonal boron nitride (hBN) and then attaching other functional groups. This means we can give hBN whatever desired properties certain companies are requesting.

These particles of hBN are captured by filtering out of solution using the following set-up.

Currently my project is to attach dimethyl acetamide to hBN with the hope of creating hydrophobic hBN.

Stay tuned for more exciting news from MATERIAL SCIENCES!!

Week 1 Recap

During the first week, I focused on trying to understand the goal of the research and how it could impact those in underserved communities. After listening to our mentor, Yongyi I learned that we were trying to develop a program that utilizes a webcam to detect vital stats such as heart rate, breathing rate, etc using photoplethysmography. We were given three articles to read to help us understand the technology and the pros and cons.

I read the articles that we were given and learned that the technology does not always work on people with darker skin tones or in low light conditions. One of the ways to combat this could be to use another source of light such as a flash or a light stand. Another way to combat this issue is to use another color channel COG – that is Cyan, Orange, and Green. Or, to use a green filter.

Side note: when we walked to the police department to receive our ID badges, I experienced the “shadow” phenomenon. When lighting isn’t conducive to darker skinned people, their features are not present in the picture. My ID picture looks like a dark blur….with teeth.

I struggled to understand the full goal of project, so I reached out and asked more questions. And this is what I came up with:

A. Construct the rPPG program – in the most basic form

B. Test out the camera on darker skin tones and in low light conditions using the following

    1. ambient light
    2. Green Filter
    3. Flash
    4. COG

C. Connect the technology to it’s application in underserved communities.

D. Develop a poster to explain all of the above.

After doing some more research, I learned that there is a general distrust among African Americans and healthcare providers. African Americans are also more likely to experience heart related issues. This technology has the potential to improve health outcomes for those that live in under served communities. More specifically, African American males. This is my focus for the application of the technology.

Looking forward to week 2!

Week 1 – FMOC Peptide Preparation

Week 1 in the Lab

My summer project primarily centers around the effect of the media on the peptide hydrogels to be used for encapsulating MSCs that for a future in vivo study. To start, we were busy making a 21-amino acid peptide using the FMOC method during the first week. The entire process can take several days. The process has alot of steps that are repeated. Viri (grad student) would do one step so I could see how to do the step and then she guided me on my physically duplicating her step. The FMOC process involved a resin (looks like beads/see picture) that holds the growing peptide. To generalize, the technique required protection and deprotection of the amine in each amino acid while its incorporated into the growing peptide. The efficiency of each step was monitored by taking a “nano-sized sample” and adding ninhydrin. After heating, test samples were generally either blue or brown indicating deprotection or protection had occurred. All the colors were appropriate so the peptide should be in its correct sequence. The crude/impure peptide should be finished with dialysis on Monday. We will use the mass spec next week to determine if the peptide is correct.We have to prepare more peptides for  before in vitro testing of the peptides in hydrogel. Viri is also growing and staining MSC cells for encapsulation.

K-12 Educators Disseminating Research from Rice University, Arizona State University, and University of Texas-El Paso