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365 Days of Academia – Year two

The recovery

A lovely stock photo showing some spine surgery. I really didn’t feel like posting a picture of my incision sites.

We’re post-op day 2 so far and the word of the day is ouch. I don’t know that I went into detail about the surgery I was having, I mean I’ve been out of it these past couple of days since the surgery. It was a spinal cord surgery, there was some scar tissue that was giving me some trouble and they went in bilaterally (both sides of the spine) to remove it. That was… fun.

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The aftermath

My anti-nausea gift, apparently it’s slow, but works.

Well I had a surgery yesterday and it didn’t go as smoothly as I hoped. I’m home now thankfully, but there were some… complications and it could be for a lot of reasons, but I’ll cover the most likely issue and then go and rest some more.

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Surgery time

Well today is the day. I just checked in and ready for surgery. For those of you who follow along, this isn’t the first surgery I’ve had. I’ve had two surgeries a year for the past four years. It’s a lot, but each one offers the promise of a slightly better life.

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Today is a bad day

The day hasn’t even started yet, but it’s a bad day. No I’m not ripping off a children’s book with a similar, if not more hyperbolic name, it’s seriously going to be a bad day. You may be wondering how I know, well this time of the year is always rough for me. A lot of bad things happened that I don’t have the space, mental capacity, or time to talk about. Today is a bad day.

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The (other) secret

whispering a secret into someone's ear.
Shhhhh….

Some days there’s just so much going on it’s hard to figure out what to write about. Daily writing is hard because some days you have 50 things you want to share and some days you can’t figure out a single thing that would be interesting to write about. While I have a million things to do, none of them are new and interesting enough to share. So today I’ll let you in on my secret.

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Technical writing: How to write gooder

Know your audience, it’s the first rule of technical writing. I’ve taken several technical writing courses during my education and they all start off the same way. KNOW YOUR AUDIENCE! In my experience that is usually the end of the advice given. Most technical writing courses assume you know how to write, an odd assumption when you’re supposed to know your audience. Today I’m going to go over what I do BEFORE I write, in the hopes that it will help some of you. Fair warning, this is long and detailed!

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The ambiguity of language

Well we made it, it’s Friday. I’ve finished my experiments, done most of the things that I needed to do and now I can focus on writing for once. No, not my blog. It’s finally time for some technical writing. I’m not thrilled about it, I mean I don’t mind technical writing as a general rule, but it does get tedious with all the edits. Maybe that’s why I like my blog so much, I can just write and be done with it.

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Yet more experiments?!

Sticky notes are the best.

Another long day for me. Back to back experiments (with a short break in between thankfully). It’s a lot, but I’m hopeful that after it’s all done things will slow down at least for a moment, hint they won’t. In any case, I just need to make it to tomorrow then I get a break for a few days.

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Surgery in a pandemic

A seemingly endless hallway in a hospital. The floors have a shine to them and the yellow tint to the lighting makes it feel older than it probably is.
I took this photo today. It’s my favorite hallway in the VA because it just seems so endless. It goes the full length of the hospital (I think) and today it was empty. They are limiting the number of people who can come into the VA, which was a nice surprise, although it was still far too many people for my comfort.

I was planning on having surgery over the summer. I put it off because I didn’t want to go to go to the VA hospital. It’s a depressing place in the best of times, a not so friendly reminder that as a veteran we’re better off dead and the living are an afterthought. When the pandemic hit it was, and is, the last place I want to be. Yet, I can’t put it off anymore, so I’m having surgery.

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A small reprieve

Well today my midday experiment was cancelled so now I have some time to relax. Just kidding, now I have time to work on the million other things I need to get done this week! That’s the problem with writing daily, a lot of it is the same stuff, but there are some minor differences with today’s list of things to do.

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A week of experiments

Don’t mind me, just trying to turn back time… lol

Most times work can be a trickle, we get one or two subjects a week and that’s all. 6-8 hours in the entire week dedicated to collecting data and the rest of the time I’m free to process data, work on other things I need to do, basically live day to day like I didn’t live in a lab. Most of the time. Sometimes it’s a flood, like this week and next, then I’m reminded that I definitely need to work.

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Catching up

This feels about right, I’ve been running on empty!

Sunday means getting ready for the rest of the week and what a week it will be. In my Co-PI’s lab we typically have a steady stream of people coming and going for experiments, this week (and probably next) it will be a flood. We’re trying to make my main-PI happy.

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A whole pile of work

Pretty much a live shot of my life right now…

Why does everything happen at once? I mean you’re minding your own business and bam, suddenly you have a million things to get done. One minute you’re on top of things, the next you don’t know how you’re going to get it all done. I’m somewhere in the middle of all that right now. I’ve managed to get most/all the things I needed to get done, but not without some new things popping up.

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Meeting a potential postdoc

Comic from phdcomics.com

Well today has been interesting to say the least. It wasn’t planned, but I went into the lab to meet my Co-PI and the new potential postdoc for the lab. I sort of rushed in last minute and the coordinator apologize, but I hadn’t planned anything that would’ve been hard to do in the lab anyway, so it wasn’t a big issue.

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Behind schedule

Well it’s Thursday and by looking at my list of things I need to get done, I wish it was still Monday. There’s been a few setbacks the past couple of days. My data processing is going well, but not much else has been accomplished because of an incident that happened a few days ago. It’s not a fun time…

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Data results!

light bulb in the sunset

About a week ago I collected some data randomly. Well let me start over, not randomly my Co-PI decided it would be a good experiment to collect the data using my “super secret” technique to verify that it worked. We had six different conditions and I’ve only processed two of the conditions, so there’s still some work to be done to determine if this is real or not, but I have my initial results and my Co-PI has seen them.

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Grant writing!

writing spelled out in letter tiles

It’s time to help write another grant! In this case, it’s one I actually want. One of these days I’ll write a little tutorial on how I like to do my writing, I think it’s a good system, but then again what works for me may not work for you. This one is particularly complicated though so it needs a lot of attention. It’s not that it’s long, it’s because it’s short.

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Dominoes

It’s going to be a busy week for me. Seems to be a theme in my quest for that PhD to be honest. I’ve got data to process, papers to write, experiments to run, appointments to keep. It’s a lot of moving pieces that all need to be aligned at just the right moment. Dominoes, if I can get everything lined up nicely, the tasks will all fall just as easy.

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The grant proposal

Well today one of my grant proposals is due. Technically it’s due tomorrow, but I always try to submit a day early. Why? Well, technical issues, I’m an anxious person, all that good stuff. This was an equipment grant and I did it at the request of my PI, it’s not the grant I want, but it’s a learning experience, or at least that’s how I’m treating it.

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Exoskeleton experiments

Just a few of the exoskeletons we have in the main lab, two of them are self balancing the other two in the shot are not, but they all have different purposes.

Well let’s toss something else into the pile of “things I’m going to talk about, but can’t share the details because we’re working on a publication.” I’ve got yet another new project I’m working on! This is going to be so freaking cool and I’m super excited to start it. So let’s go over some of the details, at least the bits I can talk about. Eventually when all this stuff gets published, I’m going to have a ton to write about.

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Experimental failure

Well that was a …flop. Today I had an experiment, had. There are a lot of moving parts when it comes to an experiment, especially in my line of research. Technology, can’t live with it, can’t live without it. Still, somedays I wish I was living in the future, one where I didn’t need to reset my router randomly. Then I would know for sure the singularity was close.

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A wild collaborator appears!

A robot… in parts.

It seems like weird stuff just keeps happening left and right lately! Yesterday out of the blue I heard from a collaborator I worked with from the UK. It’s been months since we last spoke and he had some personal issues due to COVID, so I wasn’t actually sure I would hear from him again.

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More data!

Old wooden treasure chest with strong glow from inside.
Old wooden treasure chest with strong glow from inside.

It was a surprise to me, but I somehow ended up with a new dataset from a single subject. One that, after processing, could be the key to convincing my Co-PI once and for all that we have something real… or it could just be one giant mess, but if we don’t look we may never know.

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War and (hunger) games Part 3

Well I just started book three and thought it would be fitting to have a third talk about war and Hunger Games (Part 1, Part 2). To be honest, this post wasn’t going to exist. I’ve shared my suicide attempts, my depression, my anxiety, and all the seemingly taboo bits of myself. Today I’m sharing something that’s hard even for me to talk about. In a lot of ways dreams are very personal. I don’t know about dreams, but I can tell you about nightmares. If you’re squeamish, this is your warning to turn away now.

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Problem solved

Sometimes we don’t need to think outside the box, the box can stay closed for the moment…

Everyone go back to what you were doing, nothing to see here! Yesterday I had an existential crisis, one that could’ve derailed my technique and any hopes I had at introducing something new into the world. With it, my PhD dissertation topic, meaning I would be over two years in and I would need to reevaluate my goals. Let’s talk about what happened!

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A snag

No tears, please. It’s a waste of good suffering.

You know… that’s how it goes sometimes. You’re cruising along and everything looks great then, BAM! Totally derailed. What happened? Turns out I have a problem with my data. Not a problem persay, more like an anomaly, one that throws a rather large wrench into what WAS a perfectly running operation. Things were looking good, but now… I have a doubt.

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A lot of changes!

While EEG caps look super high tech, it’s actually a low-tech solution to an environment full of electrical noise. Each channel is pre-amplified at the source to reduce contamination as the signal travels down the cable. The first active electrodes? Made sometime in the mid 90’s, so a surprisingly new advancement in the history of EEG!

Well if there was any doubt that I write these daily I’m sure yesterday’s brief post explaining my panic helped answer that question. It really was a busy day and that’s not a bad thing. Things are… changing and I can’t tell how they will turn out now, but I’m anxious to see the outcome. How very mysterious! Let’s talk about it.

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A busy day!

Well it’s been… a day, which for me started at 5am. It’s not over either! Our experiments ran long so I haven’t had a chance to get a break in between the different experiments and now I have class, so basically this is the post. It’s a busy day and I still have so much work to do! Good luck to everyone out there who is also swamped. Hopefully the weekend will give us a break!


War and (hunger) games Part 2

Obviously I’ve had more thoughts since yesterday’s post. With the fourth book just being released I’m giving the hunger games series a reread so I can refresh my memory before diving into the new addition. Sure it’s a prequel, but reading in published order never hurt anyone. Others have had the same thought obviously and yesterday’s post was inspired, in part, by someone’s take on the books. Now that I have had some time to think about it, let’s talk about the Hunger Games.

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War and (hunger) games

The first time someone asked me if I killed anyone I was taken by surprise. It’s a deeply intimate question, but a question that some people seem to ask so flippantly. It’s a taboo, even in my small military circle of friends. One that I don’t talk about and one that we will certainly not be talking about today. I’m reading, or rather rereading, the Hunger Games trilogy and it made me think about the first time I read it.

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More on mentorship

It’s dangerous to go alone!

One of the more enjoyable aspects (see: favorite thing ever) of being a PhD candidate and about half way done with my degree (… WAIT. HOW THE HECK DID THAT HAPPEN?!) is that I get to be a mentor. To be fair, I’ve been mentoring since my senior year of undergrad, but my style has developed and I don’t… flail as much as I used to when I first started mentoring students.

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Dataset mining

We use heavy equipment to mine our data around these parts…

I did an experiment! That’s old(ish) news, but now I have some data to play with… lots of data. So now I get to do something somewhat enjoyable and that’s try to get cool and interesting stuff to fall out of it. All you have to do is shake it really hard and hope for the best.

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A breakthrough

Oh yeah!

Well… where the hell do I even start? Yesterday was actually a semi-okay day. I mean the world is still on fire, the pandemic is still killing far too many people( but somehow not enough for the people in charge to care), and I mean let’s face it, it feels like the human race is in the death throes. HOWEVER, all that aside, my microscopic insignificant day wasn’t bad… now I’m worried.

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Distractions, distractions

Comic by theAwkwardYeti

Why people think that we could be MORE productive in a pandemic is beyond me. I can barely get myself out of bed most mornings when there ISN’T a pandemic killing ~1200 people a day. I mean how high does that number need to be before you too are less productive my fellow compassionate human?

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The Nyquist frequency

Parts to a wave (top left) a example wave (bottom left) and different examples of how waves change based on frequency (top right) and amplitude (bottom right)

A few days ago I realized I had never bothered to explain the nyquist frequency. Considering it’s been over a year now since I explained some of the frequency domain things that I do in my lab, I’m actually surprised I missed something so important. Well, better late than never today we’re going to explain the nyquist frequency and why it matters… to my work at least.

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Health in a pandemic

I don’t want to be another link in the chain. I’m selfish, I don’t want to get COVID, I don’t want to deal with the after effects (if I live to tell the story), and I certainly don’t want to get others sick. My travel is limited to places I absolutely need to go. Unfortunately, that means I’m stuck doing research in a hospital setting, but I mask, wash my hands, and do everything I can to keep safe.

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Thalidomide: A forgotten history

Distaval was the brand name for Thalidomide

The COVID-19 vaccine is coming… eventually. There is a push by Trump to get it out to the general public prior to the election no matter the cost… gee I wonder why? However, we have testing standards in place for a very good reason and while it can be medically necessary to provide promising medicine in a few select cases, this is not one of them. A history lesson is in order and like all history, we may be doomed to repeat it if we don’t learn from it.

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On being exceptional

If you’ve read my blog for any length of time then you know I’ve had a hard life. A very, very, hard life. The thing that keeps me going isn’t money, it’s not the chance for fame, or for people to remember me when I’m gone. The thing that keeps me from very literally killing myself is the chance to help people. That’s a selfish goal, but everything that drives us at its core is a selfish thing.

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Neuralink: Beyond the hype

The sewing machine like robot that is the linchpin for neuralink.
The sewing machine like robot that is the linchpin for neuralink.

Brain machine interfacing, as someone who does research in the field and is getting a PhD in a brain machine interface lab, I think I’m qualified to comment on the progress neuralink. There’s a lot of hype out there, curing disease, ending paralysis, a world where we are part of the machine and the machine is part of us. Is it science fiction, or is there more to it?

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Fact or artifact

Does it belong in a museum though?

A new turn in the saga of my data processing. There has been some concern that the artifact from the stimulation is causing the thing I am seeing in my data. There are arguments to be made for both sides, but let’s go over what that could mean for me.

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Path planning

One would think that the pandemic would put a lot of things on hold. Unfortunately (here in the US anyway) that isn’t the case, it just makes things harder to do because everyone expects you to perform at a higher rate now that you’re not commuting to school… how the hell that works is beyond me.

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So much data

This has basically been my progression in this project.

Well I’ve processed (poorly) about half of my data. Now, when I say poorly I just mean the visuals for it are garbage and I need to tweek the sizes and things to make it look nicer, but the idea is that I’m more interested in finding something than I am in making it look pretty. I’ve processed two of four of my subjects and well I’m excited!

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The after

I’m trying to remain calm. I am an objective observer in the world of science and whatever the result, I will NOT let it cloud my emotions. I am neutral and I will remain that way… oh who am I kidding, I DID IT! Two years of planning and convincing people this would work. Then last night I had my first result, and it was a relief. It was a small step, but one I was afraid the data wouldn’t let me make.

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Into the unknown

Time to cross that bridge…

Today is going to be a somewhat anxious day for me. It’s the day I get to crack open my data and see what spills out. There was a process to get to this point of course, it took me about a week, but today with just a few clicks I’m going to see if I have something or if my idea was never meant to be.

Read more… if you dare!

How to 3D print… yourself!

It’s hip to be 3D…?

Ever have an MRI or a CT done and thought, “I really wish I could do something with that.” Well you’re in luck! Today we’re going to do a quick rundown on how to take a medical scan and convert it to a workable 3D model. Something you could 3D print for example! As with everything else I do around here, this is done with free software so the only limitation is your access to medical scans, but we can get into a work around.

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3D Print… yourself!

It’s hard to tell the scale from this image, but you’re looking at a full sized copy of my spine. Yes, full sized as in big, really big!

You know what’s boring? Going to the doctors office and getting an MRI. You sit there forever! Of course a CT scan is faster, but there’s still a lot of waiting involved and in the end, you get to see a quick glance of the images captured if you’re lucky. Where’s the fun in that? Well I’m here to help you do something with that information. Useful? Maybe. Fun? Definitely!

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School is coming…

3D printed spinal column still in parts getting ready for cleaning and assembly.
Did I mention I 3D printed my spinal column (as in a copy of MY spinal column)? Because I did. I’ll post up an explainer how later, but here it is in pieces waiting for me to have a few free moments to clean and assemble it. In the meantime, this is the teaser image for it.

With classes about to kick off I’m left wondering what will be different for me. This term I’m doing the safe thing and taking a single online course. The rest of my time will be focused on my research and doing what I need to do to be ready for my PhD proposal defense (the step I want to take this fall term. So what am I doing to get ready?

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School and COVID-19

School being cleaned in preparation for students return. This is security theater, it spreads from student to student more readily than from desk to student.
This is security theater, like taking your shoes off at the airport, it does nothing to keep you safe. Instead it makes people feel better, in this case the school for letting your children spread this virus without a care.

School, I would like to consider myself a lifelong student, but formal instruction is a little different than learning on the job or via the web. With classes starting, my stress seems to be slowly ratcheting up. Oh I’ll be fine, I’m taking an online course this term, I’m worried about everyone else.

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A busy day!

Yep I use this image a lot, but it’s such a great representation of our labs work!

Well I didn’t plan for it, but today is a busy day! I’ve got a lot going on at the moment so not a lot of time to write. Let’s just talk about what I’ve done and have left to do so I can get back to it.

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Process the data!

This is what raw EEG data looks like. Seriously, it’s a bunch of squiggles. However, we can make sense of it and we can even write some code to make sense of it in real-time so you can control things with your brain!!! <EVIL LAUGH>

It’s a process… that’s for sure. So you’re a scientist and you collect a ton of data, well now what? We’re talking about me of course. I did it, I collected a ton of data and now I need to do something useful with it. This is the part I wish I could skip over and get to the part where I get all the cool results, but I guess we’ve all got to start somewhere.

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