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Posts tagged “PhD

Day 331: Solid modeling course day 1

20200715_134927

The dual extruder attachment, the current bane of my existence!

Well can’t complain too much about the first course. I’m used to people talking to me so it was an odd feeling talking into a screen with no one talking back. I had a few questions, but mostly the course was on how to think about solid modeling, so maybe not a lot of room for questions?

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Day 330: I’m teaching this week!

Harbinger

I love mass effect, so I really thought this was a perfect header image for the post since I am… assuming control!

Well I mentioned it a few days ago, but it’s day one of four today. I’m teaching three courses on solid modeling and one on 3D printing * Shakes fist at 3D printer who keeps giving me problems * and I figure I can talk about how my classes go after the fact, but let’s talk about my prep for these classes so my students get the most out of what I have to teach them.

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Day 329: More 3D printing issues!

Cat boss

My boss is not happy with the work I’m doing, you can tell since she didn’t want to look at me when I took this photo.

I’m giving a class on 3D printing this week and of course my printer decides it wants to throw a fit. So my print had to be stopped (18 hours in) and the printer needed a good talking to. It’s not the printers fault, maintenance happens, so let’s talk more about my poor FDM printer (Acronym defined yesterday).

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Day 328: 3D printing… ugh

3D printing

Well it’s time, in a few short days I’ll be doing a marathon session of courses for the summer interns. I admit it I bit off a lot! I’m doing three solid modeling courses, so the basics, plus a 3D printing class. Today we’re talking 3D printing because, well it’s a headache even though the prints themselves can be worth the pain. I know if I can pull off printing what I’m working on now it will be worth it… I hope.

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Day 327: Solid Modeling – Week 5

Light bulb render

Okay everyone, I had a bright idea for our sphere… get it, get it!?!

Wow, week five already! As per my usual intro, this is a free class using FREE software so if you ever wanted to create a 3D model, this is for you and all you need is internet access to use the program we will be using. Now if you are just joining you’re going to want to start at week one, which you can find all the posts in the super lovely Solid Modeling for Beginners category. We finally did it, last week we made something cool looking! Today we’re going to expand on that and use what we learned to create another awesome thing!

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Day 326: Review: The state of spinal cord research

Figure 2 from and yet it moves
Figure 2 from and yet it moves

Facilitation of stepping-like volitional oscillations using non-invasive transcutaneous electrical spinal cord stimulation in SCI subject. (A) Position of the participant in the gravity-neutral apparatus. (B) Biphasic electrical stimulation was delivered using unique waveforms consisting of 0.3–1.0 ms bursts filled by 10 kHz frequency that were administered at 5–40 Hz. (C) EMG activity of right soleus (RSol), right tibialis anterior (RTA), right medial gastrocnemius (RMG), right hamstrings (RHam), right vastus lateralis (RVL), right rectus femoris (RRF) and angular displacement in the knee and hip joints of both legs during leg oscillations with a voluntary effort alone (Vol), stimulation at T11 (Stim), and Vol + Stim are shown. (D) Schematics demonstrating the approximate location of transcutaneous electrodes above the lumbosacral enlargement, in relation to the location of the motor pools based on Kendall et al. (1993) and Sharrard (1964).

Well it’s been two weeks (roughly) and my PI asked specifically that this week I do a review on the state of spinal cord research, with emphasis on the spinal cord stimulation work I’m doing. So this review is going to look slightly different, namely it has a rather long references section (15 total). If you find this research fascinating I recommend “And yet it moves” (reference 5). It’s long, but open access and worth the read. I’m a little bias though, my Co-PI is one of the authors. In any case, I had two weeks to write this, so hopefully it is a good dip into what we know about the spinal cord and a lot of what we don’t. Enjoy!

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Day 324: Rewriting

edits

Today is a bunch of meetings and a bunch of editing. As I mentioned (or at least think I mentioned here), I had to meet with the senior author for the paper I’m working on and I got a lot of feedback, some of it was good, most of it meant more work for me. That’s the process though, write, rewrite, re-re-re-re…rewrite.

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Day 323: Skype a Scientist!

wiring

Today is going to be fun, I’ve got a ton of meetings, but I also get to do outreach. If you’re a scientist, you can do it too, no matter where you are in the field, sign up at Skype a Scientist. While I wanted to write this post before my sessions I ended up having to write it afterwards so let’s get into what I talk about and how it went.

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Day 322: Stuck

hamster wheel

Ever feel like you’re just going around in circles like a hamster in a wheel? I’ve been working on about a million different things and I just can’t seem to get them off my plate. The work just keeps going and it’s got me somewhat down. Maybe I just need a day off or something.

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Day 320: Solid Modeling – Week 4

Finished Rocket

We’re making something a little more exciting than a cube today. Yay!

Welcome to week four! For those of us just tuning in, this is a class for solid modeling using FREE software, so if you have internet access, you can do this too! You can find the whole course in the handy Solid Modeling for Beginners category. Last week we introduced a whole lot of navigation tools and helped you get situated into the world that you’ll be able to model in. So let’s get started by doing a quick recap of the past weeks and hopefully you’ve done your homework because we’re using that part today to make something more impressive than a cube.

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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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