I am very Excited to have finished!

I feel accomplished. I recognize fully that I am not an expert programming in Python or an expert in Photoplethysmography, but I have learned so much and I have achieved so much.

I can read from files and write to files.

I can use Command Line inputs for my programs.

I understand how Pulse Oximeters work and the potential for the information we get from them.

I am very happy to have participated in this program and I am excited about my presentation next week.

Here is how I collected data. There are 3 videos here showing collecting and visualization live data from the CMS 50D+ and/or the Pulse Sensor Amped.

Here is my result! I produced these plots using Python with numpy and matplotlib. The analysis supports the claim that an inexpensive and open hardware can match the performance of a commercial pulse oximeter. There is a lot of available data too.

Wow!  I can’t believe that the summer internship is coming to an end.  It doesn’t seem that long ago when I was traveling to UTEP just to find where I was going to be this summer and now I am working on a poster which sums up what I have learned this summer.  …and boy, what an adventure it has been!

When I first started on my research journey I had an idea that I would tackle the problem of algae blooms.  To start on the process I was paired with an undergraduate student and we worked on the applications of titanium dioxide paint to rid water of organic dyes.   What an amazing process that was to see, how the exposure of polluted water sources in containers with titanium dioxide paint applied could be purified… mind blown!

When it came down to my algae project, I found that I do not have a green thumb per say when it comes to algae.  When placing the algae in the titanium dioxide painted glassware the algae did in fact die… all of it dies, including the control.

So, back to the drawing board.  This week I have been working on the chlorophyll extraction practice of my algae samples after they were exposed to UV light.

Unfortunately, as the internship is coming to an end, the algae portion of my summer internship will be discussed not as the basis of my research but as future work.  No worries though, I have learned so much this summer and what I will be presenting next week I will do so with as much excitement as I have had for my algae research.

See you all next week!

This week has been an absolute whirlwind! We’re on the home stretch, friends.

So this week I’ve been splitting my time in the lab with working on my poster and getting feedback from the other people in the ball lab. Cody and Patrick have been especially helpful in the formation of the poster. Thanks guys!

In the lab, we’ve been working on getting some protein for our reactions – with varying results. This is my mentor’s first time doing this, so the first result was a vial full of dead cells. Ooops! The next batch was quite a bit more successful and there was much fanfare, and we were able to culture the cells with some help from Chi’s lab.

Next we had to lyse the cells to get them to express the proteins, then centrifuge the crap out of them. There was quite a bit of back and forth as to how we wanted to split the cells up, but we ended up splitting them into 13 vials (which required a LOT of fiddling to get the mass within one gram of each other).

After lysing the cells and centrifuging them, we extracted the liquid and got some decent proteins! Katie also set up a boronic acid reaction without any oxygen present which I thought looked neat. There’s nitrogen in the balloon, which keeps the pressure above 1 atmosphere.

I got my first draft of my poster done though, and good lord that was a lot more work than I thought it was going to be! I’m going to be relieved when the poster is printed out and I get to see it in all its glory.

During this fifth week of research, we’ve been able to move on past the purification of carbon nanotubes (CNTs). We were able to take the CNTs we put in solution with chlorosulfonic acid and make films.

To make films, you have to coat one side of a glass slide with the CNT solution. Then you place another slide on top of the first slide and move them around until the solution is dispersed.

Next you have to use a device built by a grad student in the lab to quickly shear the slides past each other. Both slides then drop into a jar of ether. The slides are removed and hopefully, you have a smooth film on each slide.

After the films dry on the slides, you gently use a spatula to push the film to the center of the slide until you have a fiber.

Once you have a fiber on the slide, you gently remove it and then twist it.

We were then able to measure the diameter of the fibers with a microscope and test the conductivity.

Unfortunately, our fibers aren’t the greatest quality. Moving forward, my mentor will be reviewing the purification process to find out if it’s damaging the CNTs. She’ll also be looking at the recipe and reactor conditions for synthesizing CNTs. And, I won’t be here to help! 🙁

Monday’s field trip was interesting! I enjoyed the presentation, the walk through the museum, and the water cycle activity with the beads on a bracelet. Waterworks Education Center is definitely a place I’d like to take my kids on a field trip.

https://www.houstonwaterworks.org/#teacherpreview

All week I’ve poured over data and gone back and forth about how to use the different graphs I’ve learned to make in Excel for my poster. Last week I was feeling great about making my poster. I sketched out my ideas and thought, “Next week I’ll just dump it all onto the slide – no problem. I got this.” Uhhh, well, I don’t got this. Here it is, Thursday afternoon, posters are due tomorrow, and my slide is still empty. I really have done a lot in a short amount of time and my mind is racing trying to figure out what to keep and what to put off to the side. Making this poster is harder than I had imagined because there so much to say and so little space!

Week 4 NEWT RET Tom Geiss

Title: I Got Nothing

This week’s title “I Got Nothing” has a double meaning. On one hand, I couldn’t think of a catchy title that refers to what I am doing in the lab. On the other hand, it refers to the fact that I gots no data from our experiment regarding the adsorption of arsenic by composite nanomaterials vs a zinc ZIF. I know I promised you guys some real Rick and Morty stuff this week. I was going to wow you guys with a story about how we were going to gather data from our experiment using a ICP-MS that would tell us how our nanomaterials had adsorbed arsenic from our NEWT fresh water media.

Inductively Coupled Plasma Mass Spectrometry or ICP-MS is an analytical technique used for elemental determinations. I could go into to detail about how “An ICP-MS combines a high- temperature ICP (Inductively Coupled Plasma) source with a mass spectrometer. The ICP source converts the atoms of the elements in the sample to ions. These ions are then separated and detected by the mass spectrometer.”¹However for the sake of brevity and for understanding by my target audience, I would say that the ICP-MS is like the sorting hat at Hogwarts. Its freaking magic that muggles would struggle to comprehend.

The advantage of the ICP MS compared to other types of elemental analysis is that it can detect concentrations of matter at the really low end of the spectrum. A typical ICP-MS device can detect concentrations as low as 1 in 10¹⁵.

So, we were all set to take the samples from our adsorption experiment to the ICP-MS in the chemistry lab at UTEP. Unfortunately, this is a complicated device and can only be run by one person here at UTEP and that person is in Europe until August. To make matters worse, on the same day, I found out that there is no Taco Tuesday at the Pick and Shovel (our version of the Servery for you Rice NEWTS). I was inconsolable to say the least.

With a poster deadline looming Mariana Marcos my mentor pulled a rabbit out of her hat and shipped our samples to ASU where a really nice NEWT person named Ariel will run the tests on Monday and email the results to us just before my rough draft of the poster is due on the 13^th.

Accurate vs Precise

I don’t know about you guys but the abstract due on Friday was way harder than I thought it would be. Here is what I leaned. When writing for a scientific publication you can’t just pull stuff out of your ass like we do during the school year for our principals who do not have a scientific background. My principal wouldn’t know a GMO from a solar eclipse and let’s keep it that way.

I finished my rough draft and sent it to Mariana Marcos, my mentor, for analysis. When reviewing it with her I realized that you really have to focus on stating precisely what you have learned from your research in the lab as well as what you have learned from your scholarly readings. Simply put, the hardest 250 words I have ever written.

Well, thanks for reading. See you next week

The highlight of my week so far has been getting to go on this Houston Water Treatment facility field trip. I think it was really well done. The whole experience was such that I could tell that it would be super engaging for my students, and somehow managed to keep me fascinated as well.I just loved the variety of methods they used to get information across. It allowed me to take it all in in a format that wasn’t boring or repetitive and engaged all my senses. It’s reminding me of how when I am back in the classroom this year, that the more modalities I can teach my students in, the better the information will stick. They really did get across the different points of why water was important, how much we use (which is always surprising) ways we harm our water, etc.

For instance, for sound, they had pipes that you could talk into and hear someone else on the other side–what they would “sound like through water”. They also had a model boat that was full of trash to demonstrate visually how much pollution is dumped into our water ways. They allowed you to taste the water the that was made there with the continual emphasis on how the quality is superior quality by the time it leaves the facilities.  They had displays that had tactile components–and they even guided us through with a scavenger hunt to find the important information throughout the museum.

I even really enjoyed the “Water Cycle” Lesson that they had us do after going through the museum portion.  It was really fun! I also immediatley started thinking about all the different ways I could implment a similar lesson in the future with other concepts that I teach during the year. As I was talking to a group of other teachers at lunch some suggested things like the carbon or nitrogen cycle as other ways a lesson similar to this could be used.

I will certainly try and see if I can schedule  field trip for my students to go to this one, especially since we have a Watershed unit in our curriculum toward the end of the year.

A display that showed how much water was consumed doing normal household tasks

A display that showed water borne pathogens in a really interesting way–as wanted posters.

A model boat and the amount of trash that you can find in our bodies of water.

This was part of the lesson plan where we got to pretend we were a water molecule and travel through all the different parts of the water cycle by rolling some die.

Loved it! Even though we were unable to tour their actually treatment side of the facilities due to their expansion and renovations–even the part that we did get to do was truly exceptional!

It was me, I admit it…I killed the algae.

So throughout the summer I have been focusing on using titanium dioxide nanoparticles suspended in resin to destroy organic pollutants.  Initially the focus for my internship was learning the process behind the titanium dioxide paint and its applications.  I had worked on it for weeks and so I thought that when I was to try it with my algae samples that it would be easy cheesy lemon squeezy.  What was I thinking?  I know better.  I know that is not how science works.

So, as I am sure that you have noticed from previous blogs I have tried putting the algae samples in glass jars which were specifically made for my algae samples.  Initially I placed them outside for two days to see the effects and the samples were in fact dying.  Trouble was, all of the samples were dying, even the control samples.  :0(
As I explained my process to the lab’s PI he gave me another idea.  He told me to expose the samples to UV but in a controlled manner and by doing so to use the UV chamber.  By doing so I could collect the samples at various times to work on extracting chlorophyll from the samples to see if there were any noted changes.  So, that is what I did!  I prepped the samples, placed them in the jars and placed them in the UV easy bake oven.  (That is what I like to call it.  Review the picture below and you will see why.)

This portion of the experiment took a bit over 8 hours.  During that time period I would take out the jars every hour, take and label a sample, and place the jars back in for another hour, repeating the process every hour.  The samples were then placed in a drying chamber so that they could dry before the chlorophyll extracting process takes place.

…and here is where my samples wait.