We're a little crazy, about science!

Posts tagged “life

Day 353: Experimental prep

Matlab

Sometimes a parfor loop in just doesn’t cut it because the things you want to do in that loop aren’t allowed (like save or load data a certain way). In those cases (see above) I can run multiple instances of MATLAB and process my data much more efficiently than if I did it one at a time. In this case I had 8 subjects that needed a rather long mathematical operation performed, so I did it all at the same time. It’s a little silly, but it worked! If you didn’t know you could do that, now you do!

Yesterday I told the story of how we got to this point, a long two year journey and next week I finally get to take the next step. It’s exciting, but it also means because of my flare-up, I’m behind on what I need to do to be ready. Not to worry though, I’m taking it slow so I don’t make whatever I have worse. What goes into an experiment like this? I’m glad you asked!

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Day 352: My experiment is coming!!

EEG Cap

I just really like how this photo came out. Here’s one of my lab mates gelling the electrodes for a pseudo-experiment. The scary looking syringe has a blunt tipped needle, we don’t break the skin in our lab so no pain, just a bit of gel to wash out of the hair once completed.

Okay I’ve got an experiment update today and I’m really excited to share because it feels real finally. I know I already wrote about some of this, but when I reread my previous post, it felt disjointed so let’s go over how we got here and what’s coming. I’m excited, are you excited? I’m excited!

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Day 351: Digital color

Online persona

Anger, after thinking about it, it was anger I felt. Not at anyone in particular, but I was angry and hurt and a lot of other similar emotions, but I was angry most of all. People kept letting me down and it took a chance twitter conversation for me to realize why I was yet again left feeling so fucking angry.

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Day 350: In construction…

extruder

I redesigned my extruder to make it beefier, this has nothing to do with the post, but I’m really proud of it and wanted to share. Haha

Well today despite feeling like refried dog poop I have to go do experiments. It’s part of the job and to be honest I want to do it even though I feel like dried monkey vomit. I could go on, but you get the picture. I do have some more good news not related to yesterday’s news. So that is the conversation for the day.

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Day 349: A story in three emails

Drowning

I was awarded something, we’ll get to the what shortly. I was awarded something and I was excited because it felt like validation of my work. It felt good to have people take notice of my accomplishments. There are precious few times in my life where I’ve got to feel like someone selected me out of a group as exceptional. Here I was being nominated for something! I was walking in the clouds. I could do anything, be ANYTHING.

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Day 347: The precipice of … something

precipice

Today is a mash of things, because frankly I still am not feeling good. My the scaly bits on my hands, face, and apparently elbows (missed that one until last night) haven’t gotten worse (yay), but they haven’t gotten better either (boo). On one hand it’s a realization that whatever is wrong with me was worse than I had thought, on the other, the world still moves forward and unfortunately I have work to do, so what’s a guy to do?

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Day 346: What is going on with me?

exhaustion

It’s going to sound like depression. I realize that as we dive into today. I don’t normally do this, but I’m rewriting this intro because I know what it sounds like. It’s not that, this is something else and it worries me. I know depression, I’m good friends with depression, this is something different so don’t tell me it’s depression, it’s not I promise. It just happens to be worse than I can ever remember right as I’m dealing with the worst flare up [of whatever I have going on] in my entire life, so it couldn’t be a coincidence … could it?

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Day 345: Undergrad research presentations

Virtual classroom

Well today is day one of three for wrapping up our undergrad/high school research experience. We had a group of about 50 I think, just in our lab and a good portion of them were high school students. Because we’re living in a pandemic, this was all done virtually! Today we get the first glimpse into how we did as mentors.

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Day 344: In which we are reminded I’m not that smart

Depression

It will pass, it always does, but for now I feel like I’ve been punched in the gut. I don’t enjoy the feeling of being average, or more than likely below average. It means I have to do twice the work for half the result. I see genuine greatness and know that no matter how hard I try, that will always be out of reach for me. What do you do when you want something so bad you would die to get it and you know you will never reach your goal?

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Day 343: On lab equipment

BrokenLaser1

Luckily this wasn’t my fault, but it does make for a good story now.

It was bound to happen eventually. We all knew it would, but we didn’t expect it to fail in such a spectacular manner. That is to say, all at once. One of the people I’m mentoring checked out some lab equipment since we had come up with a way to do experiments from the comfort (see: safety) of her home. That was the plan anyway…

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Day 342: When stress hurts

Drawing of a man with cracks forming at the back of the neck. He looks sad, looking down.

Drawing of a man with cracks forming at the back of the neck. He looks sad, looking down.

I have a lot of disabilities. Some are more debilitating than others for sure, most are just annoyances or give me weird quirks that people sometimes are frustrated with, other times get a laugh from. For the past few days I’ve been dealing with a flare up so bad I’ve never experienced anything like it in my life. It was a painful reminder that I was in fact stressed.

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Day 338: Feeling stuck, again

feeling stuck

I’ve probably mentioned this before, but I feel stuck. With the pandemic going on and the protests (Which are still happening!) I don’t feel like there has been any forward movement in anything I’ve been involved with. I hate feeling like this, it’s so frustrating especially when I feel like I’m drowning in work to be done.

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Day 319: The (dis)information age

misinformation

Look around, we’re drowning in information. It’s an overload, we literally were not made to absorb this much information all at once. News stories bombard us with new bits of it. Social media is full of it. Ads promise you forbidden knowledge with this one weird trick. It’s no surprise it’s hard to tell what’s real.

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Day 318: The why.

parts

With everything going on it’s been tough to write about just one topic. When I started 365 days, I started it with the intention of highlighting my struggles and trials through one full year of my PhD with the idea that I may (or may not) keep going for the duration of my PhD process. Then COVID hit, Black lives matter protests took off (finally), and I had the realization that I, like most people, am more than just my studies.

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Day 226: Coronavirus and the military response

U.S.S. Theodore Roosevelt

U.S.S. Theodore Roosevelt

Well I got word yesterday that the coronavirus found its way onto an aircraft carrier. For anyone who’s never seen one in person, because the pictures don’t do it justice, these things are huge. Think floating cities with the crew size to match. Inside an aircraft carrier, there are roughly 3,000+ people who work, live, and maintain the ship. The one in question, the U.S.S. Theodore Roosevelt has over 4,000 crew members and those are just the ones that need to be quarantined. This is bad for a lot of reasons. For those of you who haven’t served in the military, I’ll explain.

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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 212: A small break

It was bound to happen, with the COVID-19 outbreak, my entire schedule has been shifting faster than I can keep up with it. I was going to force myself to write today, but I need a break. I’m exhausted both mentally and physically. There is a possibility I won’t be getting my stipend from the school this month, even though I’m still working, and I have assignments due soon, so I can’t dedicate the normal hour or so I would writing.

Friendly reminder, wash your hands, don’t touch your face, and practice social distancing. Even if you’re healthy, you can infect people that are not healthy or worse, people who work with others who are not healthy. Don’t be selfish! It may seem stupid now, but if we don’t do these things then it will get a lot worse and no one wants that. We can get through this if we all work together.


Day 211: Know your spinal cord – Transcutaneous spinal direct current stimulation

tsDSC simulation
tsDSC simulation

E amplitude distribution over the spinal cord and nerve surface. The color scale on the right is normalized with respect to the maximum of E amplitude in the spinal cord.

Well after our short break yesterday with my biweekly review paper, it’s back to the know your spinal cord series and we’re on day fifty-two! If you’re here for the first time, you can find the posts in this mini-series in the neuroanatomy category. We’ve taken a few twists and turns since we’ve started the series, but we’ve covered way more than I originally planned. We’ve covered how transcutaneous spinal cord stimulation is thought to work, that post focused on the type of spinal cord stimulation I’m researching. However, there are other ways to stimulate the cord. Transcutaneous spinal direct current stimulation (tsDCS) is a different way to stimulate and today we will talk about the difference.

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Day 210: Review – Cervical trans-spinal direct current stimulation: a modelling-experimental approach

Cervical trans-spinal direct current stimulation - Fig. 3
Cervical trans-spinal direct current stimulation - Fig. 3

Average magnitude of the E-field and average amplitude of its components in the spinal-WM in all montages along the z axis. Position of spinal segments is marked on the grey vertical bar, electrodes are represented by vertical bars and active connectors are marked with letter “A”. Volume plots of the E-field magnitude in cervico-thoracic spinal-WM, brainstem and cerebellum are represented at the right of the average distribution in each montage, with the corresponding colour scales

I lied! I did know what today was going to be on, it’s the fifth critical review paper. Since my PI gets a copy, so do you! To be honest, I need to create a category for these reviews (Update: I did make a category, Critical reviews), but for now, my first looking at elbow spinal stretch reflexes is here. My second where I review modulating spinal cord excitability with a static magnetic field here. The third where I review modulating the H-reflex while walking in spinal cord injury populations. Lastly, my fourth on Motoneuron excitability during voluntary muscle activity in a spinal cord injury population  can be found here. That said, let’s take a look at my latest review.

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Day 209: Know your spinal cord – Microglia

macrophage eating a bactria
macrophage eating a bactria

We cover this in the post, but it’s so cool I had to use it for the featured image.

It’s day fifty-one of knowing your spinal cord! For those of you who just found us, fear not we have all these posts in reverse chronological order listed in our neuroanatomy category. For everyone else, lately we’ve been talking about glial cells. This came about from the post on glial scarring which made me realize we should probably define glia. There are four types of glial cells found in the spinal cord (that we know of) we’ve covered three of them already and today we are talking about the last kind, the microglia.

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Day 208: Know your spinal cord – Ependymocytes

ependymal cells
ependymal cells

Ependymal cells, which create cerebral spinal fluid (CSF), line the ventricles of the brain and central canal of the spinal cord. These cells are cuboidal to columnar and have cilia and microvilli on their surfaces to circulate and absorb CSF.

We made it to yet another milestone, day fifty in our know your spinal cord series! As usual, you can find each and every one of these posts neatly organized in reverse chronological order using our neuroanatomy category. For the past couple of posts, we’ve introduced the types of glial cells, probably a bit poorly, but they are just so complex we can only really focus on a few of the functions. Needless to say they are very important cells. Today we are talking about the third (of four) types of glial cells found in the spinal cord (and brain), that is the ependymocyte. Let’s take a look.

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Day 207: Know your spinal cord – Astrocytes

upregulated spinal cord astrocytes
upregulated spinal cord astrocytes

SNL induces MCP-1 upregulation in spinal cord astrocytes (A–C)MCP-1 expression in the spinal cord of naïve animals (A) and SNL animals at 3 days (B) and 10 days (C). Scale bar, 200 μm. (D–F) High magnification images of (A–C), indicated in the white boxes of A–C, show the dorsal horn of the ipsilateral spinal cord. Scale bar, 100 μm. (G–I) Double staining shows that MCP-1 is colocalized with GFAP, a marker for astrocytes (G), but not with NeuN, a marker for neurons (H) or OX42, marker for microglia (I). Scale bar, 50 μm. DOI: 10.1523/JNEUROSCI.3623-08.2009

Day forty-nine in the spinal cord series! You can find all the posts in this series in our super useful neuroanatomy category. A couple of posts back we introduced glial scarring, one of the problems we need to overcome to help people with spinal cord injuries. That led to the realization that we needed to introduce the glial cells, so yesterday we covered the oligodendrocytes and today we are talking about the astrocyte. Now that we have some background of how we got here, let’s introduce today’s topic.

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Day 206: Know your spinal cord – Oligodendrocytes

Oligodendrocyte wrapped around axons of several nerves

Oligodendrocyte wrapped around axons of several nerves

We made it to day forty-eight! As always, the neuroanatomy category will help you find each and every post in the spinal cord series. It’s all really good stuff! We mentioned yesterday that this was coming, we’re going to do a quick breakdown of the types of glial cells just to make understanding the glial scarring post easier. Plus it helps to understand the functions of glial cells in general when we talk about things that could go wrong. With that, let’s get into oligodendrocytes!

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