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Posts tagged “neuroscience

The next big experiment

Well things are moving fast around here, like I predicted they would this year. Of course, things are currently going better than I had hoped, but that could change. Last week was a busy one and next week will be no different, but next week is a particularly big week, because I’m going to be doing another experiment for a somewhat different project. Yep, another “big idea” experiment is coming.

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Experiment prep

Tomorrow is my first experiment! To get ready I have a few loose ends to tie up before the big day. Mostly I just need to write everything out, make a list of items I need to set up, organize a few things, the stuff no one thinks about when they head off to an experiment. Tomorrow is going to be bumpy, but the first time always is, so best to be prepared.

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The first dissertation experiment

One of my favorite photos I took years ago of my labmate gelling a participant for an experiment. The syringe holds a conductive gel, the needle is blunt tip so it doesn’t hurt or puncture the skin. The gel bridges the air gap between the scalp and cap because hair gets in the way.

It had to happen eventually! But not today, this Friday however will mark the first of several experiments I will be undertaking in the (currently) slow march to my PhD. In an effort to help people understand that experiments aren’t just something that happens at the scheduled time, let’s take a look behind the scenes at what I need to do between now and Friday to get ready. It’s going to be a looong week.

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The mental health stigma

You don’t look depressed. Chances are if you struggle with depression you’ve heard that once or twice, or dozens of times on a seemingly never ending loop. If you have a broken bone you can be diagnosed via an x-ray or CT. If you have cancer, there are blood tests or MRI scans that can catch it. If you get sick, rapid tests or PCR will tell you if it’s COVID. But how do you diagnose depression?

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The lab brain drain

Today was another proposal defense! No, not mine thankfully, but one of my labmates who’s been in the lab for some time now. As the term is coming to a close, I think a lot of us are in the proposal defense phase, which means things will be changing dramatically in a year or so for the lab. It made me realize that there was a rather large gap between those of us finishing and the new members, which means big changes once we graduate.

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The cost of research

I’m not sure why, but lately I’ve been tasked with gathering quotes for new equipment. It’s not even just with the hospital side of things either, the school side has suddenly asked me for quotes as well. I understand the logic of having gather the quotes like this, after all it’s a huge time sink, but I’ve learned a lot over the past month or so from dealing with all this and that is research isn’t cheap.

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The return of last paper

If you love something set it free, if it comes back it was meant to be. What a bunch of garbage. Well maybe just in this case. I’ve slowly gotten out from under the weight of not one, but four different first author journal papers I’ve been working on. Three of the four are published (with one going live any day now… I think?! That should’ve happened a week ago…), but one paper, last paper, has been a struggle all its own and now it’s back with a vengeance.

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3 aims, 2 experiments, 1 year

It’s now official, I have a rough timeline for everything I want to do and I’ve got the greenlight from my committee that the work I propose to do will be enough to earn my PhD. I’ve spent the past day trying to plan out the rough outline of what the next year will look like in context with all the other work I will be doing and it will be busy!

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The last project

Today was my proposal defense day and I would like to say it went well. I would like to. Kidding, I think things went okay. I’ll leave that to the handful of people who read my blog regularly to judge. My committee members all thought the work was interesting and my plan of attack was good, so now the real work begins. It’s the last project before I get my PhD.

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The main event

Well tomorrow is D-day, proposal defense day that is. Technically there will be one more defense day after that, my actual PhD defense. The difference being, when that’s all done I’ll have a piece of paper to show for my efforts. That won’t come until next year… hopefully. But in the meantime, tomorrow is the (other) big day and I’m getting just a touch nervous! After all, it’s only the next year or so of my life I’m laying out for my committee members, what could go wrong?

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An ounce of preparation

What a week. It’s only Wednesday and it feels like it’s just never going to end. There are three major events coming up this week, meaning I will be working this weekend unfortunately, but at least I made it through the day. Tomorrow will be a major event for me, dare I say bigger than my proposal defense just two days away.

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The return of big idea

I had hoped to discuss robot paper today, but something more exciting has happened so today we’re talking about the “big idea’ I had a while back. It feels like it’s been forever since I had the idea, but things were moving slowly lately so we’ve had to wait. I’m happy to say the wait is finally over! If all goes well, by the end of the week I’ll have the first dataset from big idea and I am very excited!

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The proposal defense date

Single business person untangling giant rope

Okay not going to lie I had a minor freakout the past few days. One of my committee members wasn’t responding to my emails so I could not schedule my proposal defense. Last night out of the blue, reality smacked me in the face and it occurred to me that next week was the first week I was trying to schedule and time was running out. People are busy and I didn’t want any of the PI’s to have a conflict. But it all worked out…

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New and old projects

It’s finally my chance to put my own spin on the stuff coming out of the hospital lab and I’m incredibly excited about what is coming. Unfortunately I can’t talk about it! However, I’m hopeful that this year will be an excellent year for me with regards to the research I’m doing. Things are slowly falling into place and while we’re still at the beginning, things are looking bright.

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The big rush

A while ago I had an idea, a “big idea,” but the second I had that idea the clock was ticking. Because ideas are not that unique. There is a gap in research and we try to fill that gap when we see it. I noticed a gap and because I noticed it, there’s no reason others won’t notice it as well. Now we’re in an unseen race to publish and there’s still some speed bumps in the way that are causing some issues. I’m hopeful we can get there first, but I wouldn’t be surprised if we had competition.

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The other presentation

With just a few days to work on the project, I was asked to present the data we’ve recently finished collecting at work. The presentation will happen Monday, as in three days away Monday. So between now and then, I need to process the data, make some figures (so many figures), and generally draw some sort of conclusions based on the work.

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The finalized proposal

Well today was kind of a big step, I’ve finalized my proposal, got school-PI’s approval to send it out, and now I’m just waiting for a few people to select their availability so we can schedule the actual defense. I’m just a touch nervous! I still need to modify my slides and of course practice, but we’re now roughly two weeks away from the actual proposal defense!!!

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Committing to the story

For the past few days I’ve been talking about telling a story with your data. Because at the end of the day as a researcher that’s what we do. We do an experiment and, assuming it goes well, we have a story to tell about the result we found and what it means to the people reading the paper. Ideally any good story will have great visuals to add to the story and to help the reader. Which is where I’m still stuck…

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Characterization of interlimb interaction via transcutaneous spinal stimulation

A graphic hospital-PI put together to share our results. I made the figure on the left under the methods heading, which I’m still very proud of.

I was debating about talking about this because I’m “only” the second author on the paper. Apparently I’ve gotten picky now that I have a handful of first author papers in review/published. I’m joking, but seriously, this paper has a special place in my heart and today I want to talk a bit about the science, but also the story behind the paper, because it is an interesting one!

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On the shoulders of giants

Tomorrow I’m doing something for the first time, ever. I got an email yesterday with the good news and while we don’t have all the equipment we need for the project, we can still get some good data and an early look at what the data will look like. I’m so excited I’m shaking, I barely slept last night, and my mind is swimming with the possibilities. This is what it’s like doing research on the edge.

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Big claims and big evidence

In science, ideally, when you make a large claim, you need a lot of evidence to support it. In theory anyway, in practice with the speed of the internet, claims often get taken as truth no matter how self correcting later. The claim that vaccines cause autism for example has been thoroughly debunked over and over, but the claim still persists despite the piles of evidence to the contrary. Global warming is another good example of how having a lot of evidence doesn’t mean acceptance.

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The value of clean data

Actual EEG data I’ve collected, this is “raw” or untouched data.

In my line of research we have fancy algorithms to remove outside contamination to the data we collect. The problem with collecting electrophysiological data (electrical recordings from a person) is there is so much damned noise everywhere. The problem is magnified when you collect data that have a low signal to noise ratio (meaning lots of noise, not a lot of signal). Signal in this case is the thing we’re interested in measuring and while we have dozens of algorithms to filter (remove) the noise, there’s still no substitute for data that was well collected.

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The first one

Ever look up an answer in the back of the book? The problem with research is there’s no back of the book, but typically when you do an experiment you can at least glance at research surrounding your work and make sure you’re not going completely off the rails. Because I like to make my life unbelievably difficult, and because I don’t like taking small steps forward, I’m going to (hopefully) be the first to do a few things this year. But it’s not as glamorous as it sounds.

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And then DARPA appeared…

DARPA and I go way back. Right after I got out of the military back to be exact. Not that more than one or two people even know my name (and probably only vaguely), but DARPA is the reason I’m where I am today, even if the people who helped me get here don’t remember me. As much as I love the DARPA origin story, that’s all it’s ever been, that is until today, when school-PI let me know that DARPA was paying attention.

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The IRB and committee and dissertation proposal, oh my!

Well today has been eventful! After a bunch of emails, meetings, and miscellaneous things, I have a clear shot to my dissertation proposal! I don’t want to say it’s been smooth sailing or that things won’t be rough, but I’m feeling optimistic after all the news. Since there’s a lot, I figure we can cram it into a single post as I take the next few steps to the big proposal defense day.

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The PhD dissertation proposal

Spinal column shown through a semi-transparent person
Spinal column shown through a semi-transparent person

Well we’ve finally arrived, for real this time, to my proposal timeframe. There are a lot of things that need to happen between now and when I defend my proposal, but thankfully most of those things are started or almost finished. The one thing that isn’t started… well that would be my actual proposal. Be not afraid! I’m going to have the draft done today, or at least that’s what I’m telling myself.

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A (not so) small celebration of… me

a gold star
a gold star

I can write small novels on the accomplishments of others and praise the work they do, because the work they do is worth praise. I think I come off overly flattering, but I mean every word of it because people deserve to be celebrated. Well sadly, I lack that ability for myself, but I’m pushing through the skin crawling feeling that I should delete this and write something else to celebrate a victory, or at least an acknowledgement of a win. So today we’re talking about my least favorite subject, me.

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Back in the OR!

Well we finally got approval to head back to the OR. We were having some issues with our sample size, as in we hit the max for our protocol, but after a little bit of work we’re going back! The good news is that this doesn’t just affect the project I’m working on, this means I can move forward with the other project I’ve been dying to start.

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The final push of “last paper”

Amid all the chaos that the lab visitor we had yesterday caused I wouldn’t blame the causal reader if you thought that the robot project was my only focus. Hospital-PI summed it up best when he said we’re all working on roughly four projects at any given time and I responded with, “you guys are only working on four?” Don’t get me wrong, I like it this way.

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Robot troubles…

Sixty or so hours later and I somehow finished the robot assembly. It’s been a week and a half of 12 or more hour days to get it done and I’m exhausted. Still nothing feels better than when you finish, flip the switch and everything goes exactly how you hoped. Unfortunately I’m not quite at that stage… maybe?

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Inter-lab rivalry

Still from Science Kombat, because sometimes Newton just needs a good smackdown.

There’s nothing wrong with a little competition. In the field of research you’re either the first or your a footnote, so we rush to be the first when we know that other labs are on the other labs are not far behind. Our lab knew it was coming, there was already rumblings of something big coming from another lab, but when it finally came, we were both surprised, but not exactly shocked. It’s a pretty impressive paper.

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Return of the “technique”

splatter color brain
splatter color brain

With all the excitement around here with the progress made towards making “big idea” a reality, you may think that I’ve forgotten about other projects and things I’m working on. That isn’t the case and I have other exciting updates regarding something I’ve been calling my “super secret technique” not the most descriptive name, but that’s sort of the point. It’s not “big idea,” but is sure isn’t a tiny idea either.

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The big pitch

Today was the day we pitched a proposal to two of the doctors that can help make my “big idea” a reality. It did not go anything like I planned, some of what happened was funny, some of it was horrific, but mostly it went how it needed to go. Things never go as you plan them, but this was just completely off the rails.

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A big meeting

Well I’m excited, tired but excited. It’s been a long week and that is partly because I have a meeting tomorrow to discuss a project that will be a big help in my PhD, but also a really cool project in general. We also have a second big meeting next week with some guests coming to see the research side of the hospital, so yeah busy!

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In defense of pain management

Chronic pain is different for everyone, for some it feels like razors, for others even bee stings.

Well this seems to be coming up a lot lately. One of the things about working in a hospital is you get to see a lot of different opinions and cases from doctors from all areas of expertise. It gives everyone a well rounded education and frankly no matter where you are in your career it’s always good to keep up with the state of the art in your field and adjacent fields. I’m in the neurosurgery department so we get to talk a lot about the brain and spinal cord, which means pain is a frequent topic.

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The last paper

Kind of a misnomer since this is definitely not THE last paper, but it’s paper four of four. The fourth paper in my roadblock of papers where things were coming in, but for whatever reason nothing was moving forward. Now with two of the four published and one in review again after a request for edits, I’m assuming it will be accepted (sooooon!). That leaves me with exactly one paper left and there are finally updates.

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Old student, new tricks

With a little luck, I’m a year away from graduating. It’s been one hell of a journey and I really hope I hit this goal. Still, I keep thinking what’s next and the truth is the future looks a lot like the present. It’s not just because I’m now working at a research hospital, that helps, but what I mean is that the difference between being a student and being a researcher isn’t all that different. You have to learn new skills.

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People are squishy and other science explanations

A recent blog comment reminded me of something I said the other day to surgeon-PI. Keep in mind that surgeon-PI and I have only known each other since he started at the hospital, which isn’t long. While we were doing an experiment in the OR, so under his watch, we discussed some of the challenges with the experiments we were doing and when we tried to change things on the fly he said it was bad science, to which I replied people are squishy. I said what I said damn it!

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The chronic pain conundrum

Several days ago I ran into a group of people who work with chronic pain patients. I don’t remember how the conversation got started or why we ended up discussing treatment options, probably because of the work I’m doing, but the conversation stuck with me and it isn’t for good reasons. Let’s face it pain is a pain. Frankly we need pain in our lives, but even with the best things, moderation is key. So what happens when good pain pathways go bad?

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Chaos as enjoyment

Well today’s post comes far later than I would’ve liked, but hey it’s been a day. What kind of day? Well surprise, surprise I cannot talk about it! That’s the theme, I get to hint at stuff for a year or so and then surprise everyone with the paper after the fact. But today did inspire something that I can talk about and that’s why today we’re talking about why I love research so much!

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Back to back OR experiments

I’ve had one other instance where we had two OR experiments in a single day and that was exhausting. Thankfully we had a break in the middle so that I could get everything cleaned and prepped for the next time. Unfortunately I’ve just been made aware that next week we get to try things on hard mode next week.

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Back in the OR

Oh man, I haven’t been in the OR since last year! Okay we’re only a few days into the new year, but it does feel like it’s been a bit with the holidays. That’s going to change though because tomorrow is our first OR experiment of the year. And with the new year, we have some new changes to the experiment that we’ll be trying since we’ve had over a half dozen attempts to do this right with somewhat mixed success.

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Another new project!

When I think of science, for some reason exploration comes to mind. Hence the picture for today.

In the spirit of making things as hard as I possibly can for myself I’ve gotten a new project to work on from hospital-PI. This was a known thing, but it does (mildly) clash with the idea I recently had. Since I cannot share the idea I had, we can instead talk about this project a bit and why the two will be at odds. I also have a fun update on the big idea project I came up with so I’m shoehorning it in with this post since it’s semi-related.

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The first steps to my proposal

I said this year was going to be a ride and I meant it. We’re four days into the new year and I’ve just heard back from school-PI that I’m good to submit my IRB. Since that may sound like gibberish to the non-academic and because I like to make things accessible, today I’ll explain what an IRB is, why it’s important, and why having one is somewhere between a small step and a giant leap to my PhD.

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Goals for 2022

Last year I did a post like this and I figure it was fun, so I’m going to try yet again to predict what this year will look like for me. Sure, they are the things I would like to happen, but as I found out last year what I think will happen and what does happen, are two different things. So the plan is simple, list a few things I want to get done this year and why, then laugh next year as I either fail miserably, go off on some new and seemingly unrelated tangent, or do far more than I imagined. It will be an interesting year no matter what the outcome though.

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New year, new experiments

We are an alarming number of days away from the new year. Where did this year go? Why did it suck so bad? Why was this possibly the best year we will see in our lifetimes? Why am I asking so many damned questions? Am I having an existential crisis now that the year is coming to an end? That was a legit question and not part of the running gag. I’m a man who likes his plans, so let’s look at what (I hope) is instore for next year.

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Another OR experiment

Time to dust off my scrubs, it’s back to work for me. In fact, I have been so busy with other things I don’t think I mentioned it, but today is yet another OR experiment. With how well the previous two went, I’m hopeful that this one will go well, but a somewhat alarming email from hospital-PI yesterday may throw a wrench into any plans I had.

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OR experiments, the aftermath

The good news is we have data! Lots of data, more data than you could shake a stick at, although I don’t know why you would shake a stick at anything… That’s beside the point(ed stick) though! Yesterday was not one, but two OR experiments and I have to say surgeon-PI must be in way better shape than he appears because both hospital-PI and I are exhausted!

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Interrogation of spinal networks during movement preparation using transcutaneous spinal stimulation

Rundown of the experiment (A) shows where we stimulated and what muscles we recorded from. (B) is our experimental protocol that we used. We had an auditory cue, a tactile cue (a small electrical stimulation of the foot, which causes a slight tickle) and an isometric contraction task. (C) has examples of what the evoked potentials look like and it can be hard to read at first, but the far right has a very clear example (R1 is our first stimulus and R2 is the second). I don’t go into why we used 2 pulses, but there is a reason, it’s just a bit technical so outside the scope of this general review.

That’s not the name of the paper, but that’s the general idea. We tend to take movement for granted, I mean most of the time we do it without thinking. I don’t look down as I’m typing these words, yet my fingers know what to do to make it happen. Similarly, we don’t really think about balancing ourselves when we walk, we just do it. So if I’m not consciously thinking about every step I take when I walk down the street, who, or what is keeping me going?

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Yet another rush…

It’s a familiar story by now. Tomorrow is not one, but two experiments in the OR. In fact, I’m going to be so busy tomorrow that I’m probably going to write tomorrow’s post today. The good (or at least interesting) news there is that I have a good topic lined up for tomorrow since it just happened to fall in my lap. But for today, well let’s just say there’s not a whole lot of time.

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