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Posts tagged “PhD

Day 316: Internships in the pandemic

Distance learning

For those of you not in academia, summertime means we get interns in the lab to learn about how research works in a real-life setting. We typically have them help with things that require basic skills, but lets them see how research really happens. This year, we are doing everything virtually thanks to COVID-19. This is a great thing because it really means we’re doing what we can to stop the spread while still giving students a chance to experience research.

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Day 315: Neural Engineering in a pandemic

pandemic PPE

For the past week or so my PI has been away, so I’ve had the chance to work on other projects from home. Unfortunately he returns this week so I’ve got to switch gears from protests, working from home, and undergrad mentoring back to experiments and experimental setup. As the senior student in the lab, I’ve got a lot of responsibilities.

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Day 313: Solid Modeling – Week 3

 

Sketchup planes

This course will all be taught using free software so have no fear, you can do it too! For those just joining us you can find all the posts in this series in the handy Solid modeling for beginners category. For the past two weeks I’ve been going over best practices. The reason is the tools are straightforward to learn, but how we use them is what separates someone who is learning from someone who is a pro. I have had some thoughts about what I wanted to cover this week for that reason, but this week we’re making something and by me we, I mean you! First, let’s do a quick recap of what we’ve learned and we can get started.

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Day 310: Review – Interfacing with alpha motor neurons in spinal cord injury patients

Figure 1 from the paper showing EMG recordings and the transformation using deconvolution to motor neuron spike trains
Figure 1 from the paper showing EMG recordings and the transformation using deconvolution to motor neuron spike trains

Spatiotemporal spinal maps of ipsilateral a-MNs. (A) Experimental set-up for ankle plantar flexion. (B) HD-EMG is decomposed into a-MN spike trains using a convolutive blind-source separation technique. (C) The spinal output to generate the neural drive to muscles is estimated from the a-MN spike trains.

The world is on fire, we’re protesting for a future, but today I have my review paper due so instead of writing about my frustrations I’m going to share my review. Today we’re looking at the effects of trans-spinal direct current stimulation (tsDCS) on alpha motor neurons and how we can determine that effect using electromyography. It’s actually a very cool paper, the work is well done, and it’s open source so you can read it if you’re interested.

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Day 306: Solid Modeling – Week 2

part 18

We’re back again with week 2 of solid modeling for beginners! For those of you just joining in, you can read the introduction (pre-week 1) in this post. You can also find all the posts in this series (including week 1) in the Solid modeling for beginners category. Solid modeling isn’t too difficult, but it does take time and it does mean you need to learn to think about objects in different ways. Week 1 did a great job of introducing this type of thought process and today we’re going to continue from where that left off. Let’s just dive right in!

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Day 299: Solid Modeling – Week 1

Full render

Welcome to solid modeling for beginners! Each week I’ll post some new and exciting things so you can try your hand at solid modeling. It’s easier than it looks to get started and once you do, you’ll be able to create amazing things that you can 3D print, plans to build something really cool, or maybe you just want to create some art! You can do anything you want with solid modeling, that’s the beauty of it! Let’s get started.

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Day 298: A slight delay

Delay

Well today I was planning on posting a quick tutorial for everyone who wanted to learn solid modeling. Have no fear! We’re still going to do it, but that will have to wait to tomorrow. I’ve got a lot going on at the moment and creating a good tutorial from scratch will take a bit of time. What am I doing now? Well, I’m glad you asked. 

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Day 297: Solid modeling classes, free for all!

Teaching online

Luckily teaching my course online makes it easier, not harder!

Today marks the start of my summer class. It’s a small group and while it doesn’t directly have anything to do with brain-machine interfaces (frankly none of my research in the lab does) in the age of commercialized 3D printing knowing how to solid model is an important skill that can be applied to basically anything, yes even brain-machine interfaces! Best of all, you can learn with us for free (software included)!

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Day 296: Review – Spinal Rhythm Generation by Step-Induced Feedback and Transcutaneous Posterior Root Stimulation in Complete Spinal Cord–Injured Individuals

Black and white diagram showing the front and back of a human with the the placement of electrodes over the lower abdominal area and separate electrodes over T11-T12 of the spinal cord a third image to the right shows the side of the spinal column with spinal cord to depict the location of the back electrodes with relation to the spinal cord
Black and white diagram showing the front and back of a human with the the placement of electrodes over the lower abdominal area and  separate electrodes over T11-T12 of the spinal cord a third image to the right shows the side of the spinal column with spinal cord to depict the location of the back electrodes with relation to the spinal cord

Transcutaneous posterior root stimulation: Paravertebral and abdominal skin electrode placement (this is just a portion of figure 1 of this paper.

Normally I’m somewhat excited to post these, but with everything going on you’ll have to pardon my lack of joy. However, it’s been two weeks so I need to review another paper so I’m sharing it here as well as sending my PI a copy. The study is a few years old, but it’s open access so you can read it if you’re interested. Transcutaneous spinal cord stimulation (TSS) is one part of my research in case you couldn’t tell from all the spinal cord and TSS studies and posts. I find it interesting and it gives me hope that we can help a whole lot of people living with spinal cord injury. Anyway give it a read and get out there and protest for a better world.

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Day 295: Back in the lab

whole brain and spinal cord dissected
whole brain and spinal cord dissected

“What do you mean, I look nervous!?”

Well it finally happened. We’re doing experiments again. It’s kind of scary to be honest to be working in a hospital again when the pandemic is going on and we have protests still happening. While I could do without the pandemic, I hope with all my heart that the protests don’t end until the corrupt system that caused them ends first.

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Day 292: Thoughts for the day

CS gas

Yeah, totally justified…

Well would you look at that, Seattle issued a ban on CS (tear) gas for 30 days. Yeah, you read that right, 30 days. Why 30 days? Well if I had to bet, I would bet that is exactly how long it will take before they get more. In other words they ran out. They’ve been using so much CS gas that they ran out of it. I have a lot of thoughts today apparently, so let’s just dive into a small stream of consciousness.

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Day 282: Review – Transcutaneous spinal cord stimulation of the cervical cord modulates lumbar networks

Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.
Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.

Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.

It’s that time again! My biweekly critical review paper is due for my PI. He gets a copy and so do all of you. This is a particularly interesting study that falls in line with a lot of research that I am doing, so it’s interesting to see how other groups are progressing. Overall I think this is a great study and while it is behind a paywall, I think I summed it up very well. The drawing they did (above) is awesome, especially for a scientific journal where we normally use simple line figures. Anyway, let’s get to it.

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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 277: 5 tips to survive the apocalypse

Person in gas mask and full PPE holding a globe

Person in gas mask and full PPE holding a globe

The world is on fire right now. We’re literally living in a real life horror movie. Depending on your proclivity for survival you are stuck almost exclusively inside your home. Yet, everyone on the internet, your PI, and maybe even colleagues seem to tell you the same thing, you can now be more productive! Yes, we are at home almost exclusively and more and more people are suggesting to use this extra time to be more productive. Well fuck that, instead here are my five tips to help you survive all this.

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Day 276: Survivor Bias

Mom

This is my mother with me as a baby. She wrote notes on the backs of the few photos I have. It’s surreal seeing her handwriting, but it sounds like she really wanted to be a mom. I will always regret not getting the chance to know her. She may still be alive, I just don’t know and apparently no one else does either.

I have suffered more than most. I like talking about it, especially mental illness because keeping it to myself helps no one and hurts a lot of people who think they are alone. Today I will attempt to do something I am not known for, I will concisely tell a short version of my life. I will then tell you how I succeeded despite the odds. I will tell you that I struggle every damn day, but that I made it. Then I will tell you, you probably won’t and that breaks my fucking heart.

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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 272: DI..why?! – Holes in walls

10

You may notice my wood ladder, I built it to get to the ceiling.

Today we’re going to go over a few other patch jobs I’ve had to make around the house since I’ve been here. These were intentional as you’ll see. I needed some outlets put in and in order to do that holes were made, luckily I have some photos of that portion of the work just because it was so fun to watch. While, the plugs were installed professionally, the patches were done by me.

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Day 271: DI..why?! – Awkward lighting

5

What do you do when you want to install this, but the electrical box is 8 inches to the right? Well let’s go over that!

Well since I anticipate a lot more DIY posts, I’ve created a new category for them! I’m calling it DI…why?! because every time I try to fix something, I find something else that was wrong with the way they built the home. To kick this off, let’s talk about the curious case of the cockeyed casing. Or without the alliteration, the stupid builders put the electrical junction off center for no apparent reason and we’re going to fix that.

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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 268: Review – Magnetospinography visualizes electrophysiological activity in the cervical spinal cord

Reconstructed currents of MSG from the cervical spondylotic myelopathy subject. There are two different sets of plots, the furthest left shows the electrophysiological recording taken from the epidural space and the other set shows the reconstructed currents using MSG. They agree fairly well.
Reconstructed currents of MSG from the cervical spondylotic myelopathy subject. There are two different sets of plots, the furthest left shows the electrophysiological recording taken from the epidural space and the other set shows the reconstructed currents using MSG. They agree fairly well.

This is the results of the cervical spondylotic myelopathy subject. The left graphs are the ascending spinal cord evoked potentials (this was electrophysiological recordings taken from the epidural space) by stimulation of the lower thoracic cord showing conduction block at the C4/5 disc level. The right graphs are the reconstructed currents at the midline of the cervical spinal canal (red) and 2 cm lateral (blue). The leading component (the first waveform in red) attenuated and disappeared through C4–6, and the trailing component (the second waveform in red) disappeared at C5/6. The perpendicular inflow components greatly attenuated at C4/5 (the second waveform in blue).

Another two weeks, another critical review. This time I was more critical than review, unlike the last one where I was blown away at the possibilities. Why was I more critical with this one? Well in my opinion, the authors took a baby step when they should’ve taken a leap. All that aside, it is an interesting study and one I hope has several follow up experiments. This one is open access as well, so have a read for yourself if you’re interested.

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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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