We're a little crazy, about science!

Posts tagged “PhD

The research struggle

Working in a research hospital is awesome. Things are streamlined that aren’t in academia and this was probably most apparent when I first started doing research in that setting almost three years ago exactly now. There is still a lot of red tape and things that need to be approved, ethical research is important in both academic and clinical research, it’s just handled by others instead of it all being your job. That doesn’t mean clinical research is all sunshine and rainbows though.

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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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The robot resubmission

Fact: robots who don’t get published often turn to a life of crime.

Sometimes life comes at you fast, other times you’re writing a paper and four years later you’re still looking to publish it. Publishing can be like that and while I’m not the only one with this type of story, I do believe we’re finally coming to an end of the robot paper saga. I’m really hoping I don’t have a whole ass PhD before this thing gets published, that would just be awkward.

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Robot rush

Not my robot, but I figure we’re tired of seeing the same few photos of mine.

Well we’re just a few days away from robot paper deadline and there’s still some work to be done! While robot-PI is still editing the paper, I had an unfortunate realization with some of the work I had done that requires me to go in and fix a few things. So once again, I’m doing things as hard as possible.

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The week ahead

Every once and awhile I like to highlight what kind of stuff I’m working on during the week and since there are a lot of things going on and none of them would make a very “full” post on their own, I think it would be best to group it all together and look ahead because there are some very interesting things happening this week!

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Weekend work

Weekends are historically the time where I get the bulk of the work that seems to pile up during the week done. This weekend is no different and since there’s plenty to keep me busy, I am once again distracting myself by writing. Mostly because I feel like talking about what I need to do helps me figure out the best order of things to get done. Maybe it helps, maybe it doesn’t, but I like my little system.

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Oh the things you’ll learn

I’ve been a student for some time now, roughly 15 years since undergrad (not counting “traditional” schooling growing up. Over these years there were several instances, really I would consider them setbacks, where I just didn’t know what I didn’t know. Hindsight is 20/20, but the exception for me has always been seeing personal growth.

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The work ahead

There’s work to be done and as usual when things pile up like this, I like to discuss (as much as I can) the things I’m up to. Mostly as a (semi) sanity check. I want to make sure that when I write out the stuff I’m doing or the order I’m working in that it makes sense to do it in that way. So what’s in the need to do pile today? Lots of stuff, ranging from data analysis to paper writing. The work never seems to be finished.

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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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Work goals

Today is going to be quite busy between OR experiments and all the other stuff I have going on (writing, data processing, etc.). One of those other things is something I thought would be easier than it’s turning out to be and so I figured I would talk about it today. I work in a teaching hospital and specifically I do research in lab that does human experiments. I really love it and I’ve talked about all that before, but now we’re discussing what my goals are for my employment and it isn’t as straightforward as I expected.

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The robot paper response

Yesterday due partly to the house work I was having done, I got none of the data processed I needed to do, but I had a chance to address some of the comments I got from the reviewers on “robot paper.” The response is due in just a few days and one reviewer was very thorough with their feedback, so there’s a lot to address and not a lot of time to get it done. The good news is ~94% of the comments are addressed, the only bad news is that it isn’t 100%.

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The edge of panic

I’ve got a lot going on at the moment and the more I seem to get done the more I have to do. By Monday I need to have work done that would take me about twice as long to do. If it’s one thing this blog project has taught me, it’s that I’m always one missed deadline from catastrophe. Or at least that’s the way it feels inside my brain and I do not enjoy it!

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The IRB response

That was fast. I wasn’t expecting to hear anything back from the IRB so quickly, but here we are and I have a bit of work to do. Technically we didn’t get the IRB reviewed yet, it’s only been “pre-reviewed,” but pre-review helps speed things up when the IRB meet next (in about a month) to look over the application. Since we were asked to make some modifications, this should help bring our IRB application up to standard before the IRB actually review it.

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The dissertation proposal timeline

Now we wait… There’s a lot of things up in the air at the moment, but right now school-PI is reviewing my proposed plan for my dissertation and the timeline I gave to get it all done. There’s a lot of “ifs” involved with this and I’m not sure what constitutes as “enough” for a PhD. Thankfully I know the funding I was awarded is more than I need to do so I have an extreme upper limit to the work (or what I hope is an extreme upper limit).

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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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Return of the robot paper

Logically I knew I would get a response sooner or later, I mean you submit something to a journal and you’re going to get a response. Even if it’s just a screw you, you hack. Can you tell I’ve already had several of those? Well yesterday I finally got the email about the paper I wrote on the work I did in my Masters degree days, which feels like a very long time ago now that I’m almost done with my PhD. The news is good, but I’m going to be cautious.

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Breadth of knowledge, or the things they don’t teach you

As of yesterday I’ve started turning my latest idea into a reality. While I was working I realized that I have a large skillset and most of it wasn’t obtained through the traditional school route, but almost all of it has helped me become a better student and researcher. While there are plenty of things I wish the school required for a researcher, for those of you starting out it’s not too late to think about what seemingly disconnected fields may help you do your science better.

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Real-time seizure state tracking

Since I shared one of the papers I was super proud of, I figure I can share the other one as well. Like the last paper (here) I’ll explain the concept and why this paper was important. I’ll also talk about why I think it was cool and where the idea came from. Mostly this post is for people who are interested in the work, but may not be familiar with the technical aspects so I’ll try to avoid technical terms or I will provide an explanation when needed.

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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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End of the year blues

As the year wraps up, I still feel like there’s quite a bit of work left for me to accomplish. Now to be fair, year end isn’t some magical barrier, but it is a good way to mark the passage of time and I’ve had the opportunity to do some amazing things this year, so I’m not complaining. Still, with all the accomplishments I’ve had, and there were several, why do I feel like I have so much left to do?

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The path moving forward

Pick your battles. After having a conversation with another student about their PhD plans and how soon they want to graduate, they offered that sometimes you need to pick your battles. I couldn’t agree more with that statement and when I met with school-PI a few days ago virtually to go over my big PhD plans I asked what I needed to do to finish. I needed to pick my battles.

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Double OR experiments!

It’s official, I just got not one, but two new participants for our study. This will be happening next week and the scary part is they are both on the same day, so it will be more than a full day in the OR, like 12 hours or so for the whole day. Not all of that time will be spent in the OR, thankfully. Every attempt we’ve had thus far in the OR has gotten better and better, so if the pattern holds, we should have some very good data after this next round of participants and I will have more data than I know what to do with.

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Success! Journal paper 2 of 4

Well kids, Christmas has come early! As of this morning my second of four journal papers I’ve written has been accepted for publication! Since it’s been a somewhat long and confusing road, I figure today I can remind everyone why I’m so thrilled about this paper and why this is good news for me in particular. There’s still a lot to do and more papers to publish as we go, but things are looking up!

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The fifth OR experiment

Well we did it. I finally have the first (mostly) complete dataset from a patient. Overall I think it went well and we got good data. Mistakes were made! But thankfully none of them derailed the project and overall I am happy with the outcome. Let’s get into what went wrong and what went right, because having some post surgical notes will help me next time we do our thing.

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Prepping for the experiment

Today’s the day, experiment number five. With lot of luck this will be the first full experiment we do for this protocol. It will hopefully mark a turning point for us since after four attempts we’ve yet to get a full dataset. However, I’m hopeful, but I’m also going in alone today.

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Solo OR experiment

Tomorrow will mark attempt number six to get the data we’re after from the OR. We’ve got a very unwieldy experiment to do which involves coordinating with the surgeon, but also the staff to make sure we don’t run into each other. It’s a delicate dance and if you haven’t been following along, it hasn’t been great so far.

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A not so certain future

I have a lot of health problems. If I were to dedicate a post to each we would be here awhile. They affect me in ways that I’m very aware of and sometimes I’m left to wonder if they affect me in ways I don’t always notice. Maybe my communication skills are just that awful or somehow my brain just can’t make sense of things. I feel like I’m going crazy, but it has to be me… right?

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Paper three resubmission!

This was quick even by my standards, but we’ve managed to make the changes we needed to the manuscript that came back just a few short days ago (here). I’ve got to come up with a more descriptive way to talk about these papers than numbering the order in which we did them, but that’s what I’ve been using for the moment. In any case the paper has been submitted, so what now?!

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A big idea…

You ever have an idea that you just KNEW would change the way you were doing things. Like the first person to invent a surgical robot, it was just a good idea and it completely changed the way things were done. I don’t think that this idea is going to change things that dramatically, but much like my super secret technique, I think my recent revelation is going to mean some great things for me. Lighting struck the other day and it has hospital-PI incredibly excited.

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Journal Paper three update!

Well that was fast, we got reviews back on a paper we recently submitted and they were surprisingly good for us. It’s still considered major revisions, but they gave us ten days to make the changes. Ten days as of Monday, so were about a week away from needing to resubmit. There’s some work to be done for sure, but I think we can manage.

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Fun with collaborators!

So much has been going on that I can’t even keep up with it. I was debating about what news to share, but I think we’ll talk about something I’ve had in the works for awhile now. Actually I just checked my email exchanges, this has been in the works for over a year and today we finally crossed the threshold from hypothetical to real world data collection!

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Update from the OR

I don’t share actual surgery photos online (even if I could, I don’t know that I would), but there are plenty stock photos, like this one!

No, I’m not updating this while I’m in the OR, but we had OR attempt number five as a maybe today and I have good news. We managed to get a yes at the last minute and got some interesting data. It’s all very exciting, so now I need to dig around and see what we found. For sake of remembering, let’s run through how today went!

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The art of fixing things

Me right now.

Well today has been one hell of a day. It’s a long story and we’ll get into it, but I had to once again do some car repairs. It got me thinking about others who may not have the skill to do that or other things that feel very necessary for living, but I’ve had a hard life and so you have to learn the skills that others may not have needed.

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Another OR experiment… maybe

I got a random email yesterday from hospital-PI that I didn’t understand and I’m still trying to figure out what’s going on, but it looks like experiment number five may be happening as early as Monday! It will be an early morning and a long day, but it will be worth it, assuming it happens. Like everything in my life at the moment, we’re not 100% sure that we will be able to attend.

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The BIG result

Art by: Rebecca Wright

Today I had my meeting with school-PI and I have to say it went both better and worse than I was hoping for. The good news is I’m still a member of his lab and he seemed surprisingly okay with me switching projects for my dissertation, not that the project would change much, just the funding source. Of course that doesn’t mean it was all sunshine and rainbows, because that would be too easy.

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The BIG meeting

I am a simple man. I keep my life as simple as possible because some days I can barely get out of bed. Breakfast and lunch have been the same things for years and I’m okay with that, in fact dare I say, I look forward to it? I keep my hair cut short so I don’t have to even think about it and besides the things I need like money to live, I don’t go out of my way to complicate things. Aside from my education and the things related, I have very little that I NEED to do, so I can focus on surviving the day. It’s a good system.

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To catch an error

Well it’s been an adventure! First we collected some one of a kind OR data, then because of technical difficulties couldn’t get it to open. The support team for the software has been amazingly responsive and we were able to recover the file! Or so we thought, saving the file caused the error to reoccur, so we needed more help. Thankfully because we could open the file, I could debug and now I look like a data wizard. So this is the story of how I attacked and dethroned the data gods.

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The last experiment

Goodbyes are hard, even if you don’t really know someone outside of work. Today we’re saying goodbye to a few of our participants as they finish one of our longer experiments. It feels like only yesterday, but it’s been several months now so it’s time to wrap things up. The good news is this will create a bit of an opening in my routine, but that’s probably going to be filled in pretty quickly.

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The tough conversations

One of the things I left (intentionally) off my to-do list for the week post was the talk with school-PI about hospital-PI. The plan is to arrange the meeting sometime either this week or next depending on school-PI’s availability to have the talk. I’m not thrilled about it and I don’t know how this will turn out, but it has to happen and it has to happen soon.

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Technology issues…

I’ve quickly come to regret purchasing my new(ish) fancy laptop. I get complements on it because it looks impressive and if it worked correctly it would be very impressive. The problem is that it has been causing me headaches since I bought it. Technically this is the second one, the first one was replaced and the second had the same exact issues. So instead of exchanging it again and going through that whole mess, I decided to crack it open and do the fixing myself.

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The week ahead

Semi-regularly I like to look forward at the things I want to accomplish in the next week. Having a good plan going forward helps me focus on the things that need to get done and the literal act of checking things off my list is literally the only thing that keeps me going some days. As usual I’m juggling a lot, but thanks to my 365 days of academia project, I’ve realized this, which means we can adapt… hopefully.

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