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Posts tagged “education

Day #279: Juggling (a lot of) tasks

task juggling

Since the pandemic hit I’ve had a lot of time to reflect on what I’m doing in school and things that I need to finish. Turns out I’m juggling a lot. I’ve touched on this before in other posts that I have a lot going on, but it never really hit me until recently that I have all these things and none of them seem to be ending. It’s kind of frustrating and extremely anxiety inducing.

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Day #278: Teaching… virtually

virtual teaching

We are about to start the big summer internship program at school. I’m actually kind of excited about it. I enjoy teaching and mentoring and this is just as much a chance for me to learn as for the people I work with. However, this year we are doing it all virtually, so there are some growing pains and a lot of challenges that come along with this. Let’s look at what I will be teaching this year and how I’m going to deal with the need to teach virtually.

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Day #275: Summer Mentorship

planting a tree

It’s summer, so we’re taking a break from my DI…why?! series to talk about my favorite thing about working over the summer. We get to do mentoring! As you may recall, mentoring is my favorite part of the job. Over the summer we get students from high school, international students, as well as undergrad students from all over the place to visit our little lab.

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Day #270: The to-do list

transam

When I say I lived in my car, I really did. This was my 84 trans am, I bought it for $600 after I got out of the military and immediately drove it cross country (like >3,000 miles). It doesn’t look like much, but it kept me dry when it rained and I absolutely loved it.

Well I’m making a list… and checking it… twice? Sorry, I couldn’t help myself. Well here we are at the precipice of something interesting. I want to show everyone that you can have a life and a PhD at the same time. Or in my case a hobby or two, maybe not a life, I don’t have one of those, but that wasn’t because of the PhD. Anywho I digress. Buying a home is a lot like buying a used car and today I will explain why!

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Day #269: A preview of the weeks ahead

two old school box style robots on a table near the beach looking at the water in the distance
two old school box style robots on a table near the beach looking at the water in the distance

Robots don’t need to social distance, but we do, so no beach trips for me this summer.

Well we’ve officially transitioned to the spring/summer break. Since I am doing my own little 365 days of academia challenge, it’s important to point out that there will most likely be a marked change in the content. So let’s look at what we’ve done to this point and what will be coming up! I’m excited, are you excited? I’m excited!

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Day #267: The problem with exams

test anxiety

I like to take my anti anxiety medication with a light snack thirty minutes before the exam. That way I get the full effect from the meds at about 30 minutes into the exam. The effects don’t last long enough to make it the entire exam, so I split the difference and this gives me the best result since I can’t stop half way and take more. Unfortunately, they don’t help, they never really do. I feel jittery, like I had too much coffee. I can’t remember the things I need to know and screw up even the simplest parts of the exam because I’m more focused on keeping my heart from exploding out of my chest!

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Day #266: Pandemic research pressure

Pandemic

Think of research like the post office, nor rain, nor sleet, nor snow, nor pandemic, we will be there working. My dumbass had to make the transition from design to human experimenting the year before a pandemic. I could be safely at home designing cool robots in solidworks, but no we need to collect human subject data and despite the pandemic, I’m feeling the pressure.

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Day #265: The lazy goals

prototyping a microcontroller on a breadboard. Random bits of wires can be seen around the black table.

prototyping a microcontroller on a breadboard. Random bits of wires can be seen around the black table.

A “for fun” prototyping project, I thought would be appropriate cover art for the topic at hand.

It’s the end of the term for me. This will be the end of the second year of my PhD program, we have officially started the big countdown to the end of 365 days with (depending on how you want to count) 100 days left, and despite the pandemic, I am making my lazy goals. Mental health is important and my lazy goals help with that, I’ve mentioned lazy goals before, but let’s talk about it in detail.

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Day #264: Summer Research

EEG cap

Pay no attention to my messy desk… instead look at the cool EEG cap I set up.

It’s supposed to be a busy summer for me. With the pandemic going on, I’m not sure how that will play out. Since we don’t know yet, let’s talk about how it was planned and then we can discuss how that changed thanks to the COVID-19 pandemic. This may be bad as far as my research timeline… maybe.

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Day #263: The Reliable Narrator Fallacy

tell tale heart

True! –nervous –very, very dreadfully nervous I had been and am; but why will you say that I am mad? The disease had sharpened my senses –not destroyed –not dulled them. Above all was the sense of hearing acute. I heard all things in the heaven and in the earth. I heard many things in hell. How, then, am I mad? Hearken! and observe how healthily –how calmly I can tell you the whole story.

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Day #262: A Brief Repose

Legion

A project from a few winters ago in my old home. My workshop was so organized!

A friend once described me as, “a maker if there ever was one.” If you ask me, he was being overly kind, but it’s true I enjoy making things. I’m always looking to learn new skills or sharpen old ones. In fact, I’m taking up some “light” woodworking over the summer to do some custom pieces for my home. It will be a fun task, if not a bit tedious and time consuming. I have a list of projects you see, but not a lot of time to do them.

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Day #261: On Being a Mentor

Tree

One of the many hats I wear as a PhD candidate is my mentor hat. It’s probably one of my favorite jobs and I get to work with some truly brilliant people from all types of backgrounds. I’ve had the chance to mentor a small handful of people and I always look forward to learning from them and through our interactions, in that sense, it’s a mutually beneficial relationship.

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Day #260: The thing about endings

The end

…and thus our mighty hero slay the beast and rode off into the sunset to live happily ever after. But why? Have you ever really thought about the way some stories choose their endings? Our hero goes through live altering and extremely daunting challenges only to brush it off like he caught the wrong bus. Pardon me, but what the actual fuck?

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Day #259: The Postscript

Sleep

After awhile you supposedly end up resembling your pet, I think it’s happened. She looks how I feel.

I just want to sleep for fifty years, is that so much to ask for? The deadline is gone whence it came! That does not mean it wasn’t a fight to the end or that there is a weird stillness permeating the house like a calm after a storm. What is it about things ending so abruptly that throws a person into a spiral of confusion?

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Day #258: The deadline

Deadline

It’s here.

If you’re reading this, then it is already too late. It’s here, do you feel it? It’s in the house… the deadline. It’s a sneaky dark and evil thing from a time forgotten, but you can feel its presence long before it arrives. It whispers in your ear as you sleep, or did it? Of course, there isn’t anything there for real, right?

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Day #257: Tomorrow…

Sisyphus

Well we’re up against the wire now. Tomorrow is the due date for my paper and with it the video I am working on. Will I make it? How much work is left to do? Why am I talking in questions? Find out more… now…?

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Day #256: Two days left…

cookie monster

A live shot of me waiting for my data to finish processing

Well here we are and it’s… ♫ the finalllll count dowwwwwn!! ♫ My paper is due sunday at midnight and between the video I need to make, the data that still needs to be processed, and a shitty team mate who has done absolutely nothing to help, well I’ve got my work cut out for me.

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Day #255: The impossibility of complete knowledge

Magic-spells

Have you ever tried to learn something and you just can’t seem to get it to stick in your brain? That would be my life, well most of my adult life since I left the Marines. There is just so much knowledge in the world and wrapping my brain around even a fraction of a fraction of a fraction of that knowledge seems to be an impossible task. So what is one to do?

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Day #254: Review – A Brain to Spine Interface for Transferring Artificial Sensory Information

Fig.1 of paper showing drawing of implanted electrodes and the two experimental setups for the rat.
Fig.1 of paper showing drawing of implanted electrodes and the two experimental setups for the rat.

Experimental setup for artificial sensory discrimination using DCS and brain-to-spine interface. (a) Rats were implanted with recording electrodes in motor cortex (M1), somatosensory cortex (S1) and striatum (STR) and dorsal column stimulating electrodes in the thoracic epidural space.  (b) Behavioral setup for artificial sensory discrimination using DCS (c) Setup for the brain-to-spine interface consisted of two modified aperture width tactile discrimination boxes.

If you ever were to read one of my review papers, this one’s for you. It’s so awesome and falls in line fairly closely to the things I want to accomplish, albeit going a different route to get there. I’m super excited to share this with all of you and I hope I did the study justice in my summation and while I admit, I had far too much enthusiasm with this one, it shouldn’t take away from just how amazing this is, see for yourself! The study is open access too, so if you want to know more details, you can go take a look!

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Day #253: A race to the finish

finish line

Well still quite a bit of work to do and some of it was frustrating, but here we are. So let’s run through what I’ve got left to do before the end of the term (ALREADY?!) and talk about the next few posts since I have somewhat of a plan… for once.

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Day #252: Dead…line

dead...line

Today is the day, my group presentation is due. Is it done? Well… sort of? Okay not quite, but we’re getting there. My group member still sucks, but since I yelled at him (in a professional manner of course), he’s gotten a little better and has been more responsive, so what’s the hold up? What a great question, let me explain.

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Day #251: Deadline tomorrow

deadline

Well the apocalypse can’t stop the gears of education. Tomorrow is our final presentation for the class I am in, so there is work to be done and expectation maximization will come another day. For now let’s give a quick rundown of what I’m working on.

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Day #250: Maximum Likelihood Estimation

probability

If we are going to talk about expectation maximization (now that I’m done complaining for a bit), we are going to have to introduce the idea of maximum likelihood. It’s going to be very easy to introduce, but it is a very powerful tool in estimating the state of something. Of course, it takes understanding a little bit of statistics, but trust me, if I can understand it, so can you.

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Day #249: A stern email later…

angry

Photo of me responding to his email …

I don’t want to jinx it, I really don’t, but I have an update on my group member situation and it isn’t completely awful! I mean, I’m still doing all the work and blah, blah, blah, but I’ve got an interesting story and I hope that things will be better now.

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Day #248: A Virtual Conference

background

Every zoom meeting I try to break my PI and get him to laugh, this was my last attempt, still nothing… my work continues.

This will be my first conference since the pandemic and it will be a virtual one. To be completely honest, it wasn’t until yesterday that I was reminded we had one today. It’s a little bit different from our normal routine and I think that is what is throwing me off.
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Day #247: The Kalman filter – Part 2

Kalman filter estimate

The Kalman filter converges on the optimal state estimate using noisy measurements and a model that we create.

Okay I lied, I think we can do a better job explaining the Kalman filter, more importantly I have a fun little demo I can share with everyone. It’s not mine, but I like it a lot and it will give you a feel for what the kalman filter does. So let’s get started!
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Day #246: The Kalman filter

We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.
We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

This is just one application for the Kalman filter, I estimated a two dimensional position using a random walk model. We have 3-dimensions here even though it is a 2 dimensional problem, the third dimension is time. This way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

Since we’ve been talking a lot about it, I thought it might be a good idea to formally introduce the Kalman filter. This will be a semi-high level introduction (like my knowing your spinal cord series), but at the end of it you should have a relatively good feel for what a Kalman filter is.
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Day #245: Fine, I’ll do it myself.

Thanos - I'll do it myself

I will not fail this class becuase of a shitty team member. I will not allow it, I’ve put too much effort and time into this class to do poorly at the last minute because my team member can’t be bothered to do the job he agreed to do. I suppose, this was… inevitable

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Day #244: The end of the term!?

end of term

Okay, where the hell did that come from?! It’s almost the end of the school term. WHAT THE HELL!? It feels like we just got started, but my instructor just sent out the final assignment, which is due the last week of school… next week. I’m sort of freaking out right now.

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Day #243: Deadlines approaching!

deadlines

It seems like it’s been non-stop for me left and right. I have experiments to do, papers to write, and classes to work on. With the pandemic I was hoping to get a chance to take a break, but nope it seems like I’m even busier than normal. I HAD thought that I was caught up finally when I finished processing some of the experimental data I had laying around, but nope I was reminded yesterday that I had not one, but two major deadlines coming.

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Day #242: Experimenting in the time of a pandemic

Experiment-blur

Another day forward in our new normal. I’ve left the house exactly once in the last two weeks and while it’s nice not having to commute to school, I do miss living in a world without the constant fear of catching the virus. What day is it? Who knows, it doesn’t matter anymore. I do have some things coming up though, so let’s talk about experimenting in the age of COVID-19.

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Day #241: Modeling the COVID-19 Pandemic

COVID-19

COVID-19

Today is the day. I submitted my super high level explainer video on how I modeled the COVID-19 about  a week ago and I got an email from my professor telling me that it was great (yay) and that she had uploaded it to her labs youtube channel. That means I finally get to share it with all of you!

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Day #240: Conferencing at a distance!

video conferencing
video conferencing

Not everyone has access to such luxurious setups.

It’s that time of the year again, well one of two times of the year really (for us anyway). Unfortunately with the coronavirus conferences are better held virtually than in person. While I have mixed feelings about the usefulness of meeting virtually to share our work, I am grateful that there are workarounds, don’t get me wrong, but there are some logistics that make it, well painful and some things that make this worthwhile.

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Day #239: Review – Burst-modulated waveforms optimize electrical stimuli for charge efficiency and fiber selectivity

Example processed nerve responses during stimulation trials.
Example processed nerve responses during stimulation trials.

Example processed nerve responses during stimulation trials. The individual CNAP responses for each stimulus (thin traces) were averaged (thick trace, n=20 stimuli). All traces are shown from time 0 to 6ms. The top trace corresponds to an amplitude of 0, the bottom 1mA, and the traces in between are arranged in increments of 0.2mA. Peak latencies and heights (o’s) and widths at half peak height (x’s) were extracted from the averaged signal. The peaks labeled for the 0mA trial are due to noise and baseline activity. These peaks are not actual response peaks from the nerve and are ignored.

Another two weeks, another critical review and as always since my PI gets a copy, so do you. Technically this should’ve come yesterday, but I really wanted to follow up with the Roosevelt mess going on. In any case today we are looking at something not quite spinal cord stimulation, but has applications in the spinal cord stimulation field. Let’s take a look!

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Day #236: Ugh, coder’s block

coder's block

Okay, maybe not just coder’s block, but I feel like I’ve hit a wall. Every homework assignment I’m given for this class includes a “create your own problem and solve it,” element and for the first two assignments I feel like the topic sort of found me. We can talk about what those two projects were, but let’s first talk about this latest assignment.

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Day #235: Video making issues

microphone

microphone

I’m not normally one for making videos, in this case I have to make (or rather narrate) two videos for this class. The first one was for our big class project and the second was explaining the COVID-19 model I created. It turns out narating isn’t as easy as it looks, even with a script.

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Day #234: Learning… at a distance

distance learning

distance learning

Believe it or not, I don’t mind the quarantine. I mean sure going out without the fear of catching the coronavirus is nice, but I’m not generally a social person. There is one thing that has taken some getting used to however, that would be the education portion of the quarantine. Distance learning isn’t particularly enjoyable for me and I’m fairly sure I’m not the only one.

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Day #233: Coronavirus modeling – Part 6

DeathsModel-NEW

Model estimated death rate plotted in blue compared to the actual death rate plotted in purple. The model predicts deaths based on the previous infected datapoint, so it’s only predicting 1 day ahead, which is not very helpful. However, it lets me check that my model is running correctly.

Another day another unfortunate datapoint for my model validation. On one hand it’s good to be able to further validate my model, on the other, it’s heartbreaking to see it coming to pass. My model prediction isn’t pretty and the trend so far has been very similar to the model. Let’s talk about how we validate the model.

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Day #232: Coronavirus modeling – Part 5

SEIR flowchart

Well I did it! I finished my model to the best of my abilities. There are a few things I wish I had time to change or do differently, but I think that just comes from actually doing it and not having a clear idea of how I wanted to do it when I started. Let’s take a little look at some of the outputs from the model and I’ll talk a little bit on what the model is designed for, it’s limitations, and the things I wish I could’ve done differently

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Day #231: Coronavirus modeling – Part 4

Deadline

Still working on my model. It’s taking a little bit longer than I wanted it to take, but I’m getting somewhere finally… I think. In any case, I don’t have a lot of time for an update. So for now this is it. I’m making progress, but I still need to get it done before my deadline, which is fast approaching. Hopefully I can manage before then. Back to work I go!


Day #230: Coronavirus modeling – Part 3

Models

Comic by: XKCD

Well today will need to be short. I broke my model… on purpose, but it still broke. That means I need to go back and check my equations, make sure my assumptions are correct, then figure out why the heck I’m getting the results I’m getting. I have a good idea about what the problem is, I’m just not sure how I want to try to fix it.

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Day #229: Coronavirus modeling – Part 2

Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.
Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.

Here we have my estimated exposed population vs the measured infected population, the exposed population is calculated two ways, the first using our susceptible population dynamics (blue) and the second is using our measured infected rate (orange). This is compared to our measured infected since we would expect to see a much higher exposed (asymptomatic) population than infected (symptomatic) population, which we do.

I’ve made a lot of progress! Unfortunately, my model needs some more work and the code is pretty messy right now. For now, I’ll share some of my outputs and discuss what I need to do to finish my assignment. It turns out I have a few extra days to finish the work, I thought it was due Monday, instead it is due Wednesday. The slides and write up are going to take the longest so I’m still crunched for time even though I am mostly done. Let’s go over it.

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Day #228: Coronavirus modeling – Part 1

Coronavirus modeling

Well the CO of the Roosevelt just got reprimanded just like I predicted. Ever predictable as usual, thanks military. In any case, that isn’t what we are talking about today. Today we are discussing the coronavirus model I’m creating, why it’s important and why no one should believe a model. I’m being slightly facetious, but read on and I’ll explain. I’ll even share some of my model results, it’s not finished, but I thought it would be interesting to share anyway.

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Day #225: Class presentations

Presentation

Presentation

For the past week we have been utilizing online resources so that classes can continue while we are all social distancing. While this is means that we mostly use Zoom, we also have message boards and other resources that we can use. However, these resources are sometimes a poor substitute for in person classes. This is especially apparent when we have certain assignments for the class, such as a group presentation.

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Day #224: Review – Cortical and Subcortical Effects of Transcutaneous Spinal Cord Stimulation

Figure 1 of the paper showing the experimental set-up and the type of pulse used for stimulation
Figure 1 of the paper showing the experimental set-up and the type of pulse used for stimulation

Experimental set-up. (A) Participants were comfortably seated in a customized chair during transcutaneous electrical spinal stimulation (TESS) or sham-TESS for 20 min. TESS was delivered using a surface electrode on the back of the neck between C5–C6 spinous processes segments (cathode) and a surface electrode in each anterior crest of the hip bone (anode) using a custom made 5 channel stimulator (BioStim5, Cozyma). Electrophysiological and behavioral outcomes were tested before (Pre) and immediately after, 15, 30, 45, 60 and 75 min after the end of the stimulation or sham stimulation period. (B) Schematic representation of the type of current used during TESS. We used 5 biphasic pulses at 5kHz with each biphasic pulse lasting for 200us. The middle scheme shows the blocks of 5 biphasic pulses passed at a 30Hz frequency. Lower part of the schematic shows the number of pulses delivered in one second.

Well it’s been two weeks since the last critical review so it’s that time again. As usual, my PI gets a copy and so do all of you. Since I’ve done several of these now (this is number six) I have a category just for these reviews called critical reviews. This is a really new study which tries to help tease apart what we are actually stimulating when we apply transcutaneous spinal stimulation. I think it’s a super interesting paper and I hope you do as well.

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Day #223: Hell is other people

From Dante's Inferno, a drawing of Lucifer in hell
From Dante's Inferno, a drawing of Lucifer in hell

15th century art impression of Dante’s Lucifer from Inferno

Sure, Sartre didn’t mean that hell is literally other people, that is a common misconception and therefore the quote is often misused. However, I’m misusing it on purpose because right now in my situation, hell really is other people. Did I mention that I hate group work? I really do and as a change of pace I’m going to try to explain without the tangents I tend to take because it’s going to be a fairly long story.

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Day #222: We’re still experimenting…?

Uncertainty

Yesterday we did science. It’s a weird feeling to be doing science when there is a pandemic going on, but I actually enjoyed it. There is something about being in a small(ish) windowless room and getting to tune out the rest of the world for a few hours. Yes, I said a few hours, experimenting takes time. Things are in flux though, even for me when I seem to have the most consistent schedule out of our lab.

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Day #216: So I’m “essential” now…

pandemic

Fun fact, I love pandemic movies. Movies, not so much living through one. As humans we are selfish, greedy, prone to panic, and for being “evolved” we are so very, very stupid. Basically every dumb choice you see the characters in those movies make while screaming, “you idiot, that would never happen in real life!” Well, it’s happening and wow does it do a number on a persons mental health. But hey guess what? I’m essential, so let’s figure out what that means in a time where the world is practically on fire.

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Day #215: What now?!

look ahead

Social distancing is important, but maybe not this distant…

Well if you missed it, yesterday was our final post in the know your spinal cord series. I’m not crying, you’re crying! Now the question is, what does that mean for the blog? An excellent question, one I wish I would’ve asked myself!  Let’s take a look at some of the things that we will (probably) be discussing now that our designated topic has run its course.

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Day #214: Know your spinal cord – The Recap

motor neuron histology

It’s day fifty-four and we’ve hit the end of our journey for this mini-series. For one last time, you can find all our posts in the neuroanatomy category. Everything comes to an end eventually and today I think we should do a small wrap up. This isn’t just a repeat of everything we went over though, we’re going to attempt to tie a lot of the topics together. So let’s give this a shot.

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