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Posts tagged “science

The long road to the end of my dissertation

Sometimes you’re so focused on something that when you take a second and look up you realize it’s almost the end of the year and you’re wondering how the hell that happened. It feels like just yesterday summer had started, we had our interns at the hospital and I had just defended my dissertation proposal. Now we’re roughly 8 months to the dissertation defense deadline and there’s work to be done. But there may be more, depending on how things go.

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Success! 2 of 10 dissertation experiments

Well today went better than yesterday and yesterday went pretty good to being with, so I’ll take it. All in all there were some things that I needed to iron out and a few things I still need to figure out, but it was successful and that’s all that matters. Since yesterday I already went over the rough outline of how it went and doing that again would be redundant even for me, I figure we can talk about how even the best laid plans can change once you start experimenting.

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Success! 1 of 10 dissertation experiments

What a day… I’m so exhausted. It’s been such an overwhelming amount of work, but it’s over and that’s one of the ten experiments I need (for the first phase of my dissertation anyway) done. The data collection went smooth, I love the new equipment, and I only ran into what appears to be one problem with the recording, but I’m hoping it wasn’t a real issue. So quick recap of how it went and then I get to remind everyone, and myself, that I get to enjoy doing it all again tomorrow!

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Experimental preparations

Finally. I’ve got not one, but two dissertation experiments lined up one for tomorrow and one on saturday. It’s going to be a busy few days and there’s a lot of prep that needs to happen today and ostensibly tomorrow before and after the first experiment. Since I am in the habit of sharing my process, I figured it would be a good idea to talk about how we set up for experiments. I’ve spoken often about how long it takes, but I can’t find a recent example of going over what that actually entails. This will be… interesting.

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Race to the deadline

What is it about self-imposed deadlines that feel more important than the ones you hardly have control over? Maybe it’s because I’m competitive or maybe it’s just that I hate failing at something that I set for myself, but whatever the reason tomorrow is my latest deadline and I’m so close to finishing I can taste it. So today I’m hoping to finish my coding work so I can process some more of the “big idea” dataset I collected several weeks ago.

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Attack of the code

Here’s the thing, all code is bad code. Some code is just better than others. For every person who writes a program, there’s someone else who would do it a totally different and, to them, less complicated or confusing way. However, as long as the code you write works, it shouldn’t really matter how badly it’s written, right? To me the difference between bad code and worse code is comments. The frustrating thing about taking apart someone else’s code is that there are rarely enough comments to figure out what the hell is going on.

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The first equipment test!

It’s been literally months in the making, but we finally have the equipment I need to start my dissertation and even though it’s the weekend, I’m making a special trip to campus (it’s been like a month since I’ve been there) to test out the equipment and get things ready for my first set of dissertation experiments! I’m hoping things go smoothly so that I can get the data needed, but as with all things, some assembly is required.

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The last day of summer internship

Today marks the big day! It’s the last day of the summer internship at the hospital and the two individuals we got to work with over the summer are about to present their final work. It is going to be a busy day for everyone involved, myself included. Since I haven’t got to talk about our interns this year, I thought it would be great to go over some of the stuff we did with them.

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Return of the experiment gremlins

Maybe the moon was not in the correct spot. Maybe the earth’s tilt was not optimal. Maybe we should’ve just called it a day. But for whatever reason, anything that could go wrong, did. We do our best to prep for these kind of events, but some days, nothing goes right. Today was one of those days and as frustrating as it can be for the experimenter, I’m sure our participant wasn’t thrilled about the constant problems either.

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A small step towards graduation

Well the hurry up and wait phase is over. As of today I now have the equipment I need for my dissertation experiments so it should be full speed ahead with data collection. Now I could do data collection and analysis simultaneously, but I don’t think I want to do that since I’m in a hurry and I’ll explain why in a minute, but now that I have equipment we’ve made a small step toward finishing this project. There are some things still lingering, but I think we’re on the right track forward. The only question is, can I get it done in time to graduate in the spring?

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A wait off

See what I did there, again? Yesterday I lamented that I was waiting, and waiting, and waiting, but Godot never seemed to show up. Wait wrong story. But seriously, I have been waiting months for equipment so I could start my dissertation data collection. THE final thing. I can’t begin to put into words how frustrating this whole process is, I’m ready to do something, like now! I want to do it, the will is there, but the equipment isn’t. So what to do, but wait and wait some more, unless…

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The wait of it all

See what I did there? As we are now at the end of the month, I’m starting to stress, yet again, about my dissertation experiments. Because life isn’t stressful enough after the past few days, my brain has decided to focus on yet another thing outside my control. But as with everything my brain does, writing it out helps, which is why we’re going to talk about what I have left to get my degree and how I’m anxious to get started.

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Presentation work

Despite all the stuff that’s been going on the past few days, I’ve been tasked with making a video for school side of the two conferences I need to attend. It’s not a bad thing, but there’s some extra work involved and there’s a bit of a timing issue. No one said doing all this at once would be easy. Even with all the stuff going on, we’ve got work to do.

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Summer intern presentations!

Okay, I’m slacking, but with everything going on these days, I haven’t really written about our summer interns. This year our interns were a little more prepared for the program than the series of unfortunate events that occurred last year. Overall it’s been a good summer session, but it’s not quite over yet. Next week we have our summer symposium where the interns will do one final presentation on the final day of the program. Which means it’s once again 🎵 the final countdown🎵!!!!!

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Death, consent, and Einstein

Actual slices of Einstein’s brain

Death and taxes, the two constants of the world. I think some people are afraid of death because it’s so common, so… pedestrian. We all do it, wealthy, poor, unlike almost everything about life, death is the great equalizer. In life we are taught we have choices and those choices are set by our circumstances, but for the most part we get to decide what our lives look like. Unfortunately, that isn’t always the case when we die, even when our wishes are made explicit. This is the true story of the death of Albert Einstein and if you don’t know it, I don’t blame you if you don’t believe it.

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It came from the fifth dimension!

Programming, you either love it or you hate it. Okay, let’s be honest, you either hate it or you tolerate it. There’s just so much to keep track of and as you start tacking on more and more, it can quickly become overwhelming. What’s worse is when you don’t have a whole lot of time to make sense of it all, you just push ahead as quickly as you can. Something has to give, it’s just a matter of what.

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The mechanisms of depression

Art by the incredibly talented DestinyBlue

In news that will surprise almost zero depressed people, we are once again adjusting our thought process on what causes depression. But in an effort to stave off bad advice, people telling you to stop taking your medication, and just general confusion, let’s do what we do best and talk it out. First, let’s be clear, don’t stop taking your meds, it’s never a good idea, I promise, 10 out of 10 times it’s a bad idea unless you’ve spoken with a doctor or are having serious side effects. So let’s talk about the latest news, shall we?

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The long wait

Soooo… my dissertation. Haven’t really talked about that in a bit. Yeah, things are off to a rocky start. In the spirit of being transparent and sharing all the struggles, I figure today we can discuss where I am in the process. That includes the hold ups, the let downs, and why I’m officially just a bit nervous that I’ll actually be able to meet my goal of graduating in the spring. It’s going to be a bumpy ride, but at least it’s temporary, he says as if he actually believed it.

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Fantastic posters and how to make them

From the ever accurate PhD Comics

It’s that time of the year again, time to make a poster! I’ll be doing at least a couple this year to display some of the work I’ve been doing, but the current one I’m in the process of finishing up is for the summer conference the hospital holds. They sent out a template and a example poster from last year’s event, but the example was bad. Like really bad. So maybe we need to talk about what makes a good poster, because apparently people think they need to be books.

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A forgotten paper

Well it happens I guess, after looking through my posts, I haven’t seen one where I discussed another paper I’m working on (because there always seems to be many). I am like 82% sure I’ve mentioned it in passing, but I can’t find a post on it, so today we’re talking about the forgotten paper. Don’t worry we’ll come up with a better name before I finish the post, but for now let’s talk about why it slipped my mind.

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Conference update!

Vector illustration of a person speaking to a large crowd of people
Vector illustration of a person speaking to a large crowd of people

A few weeks ago I submitted an abstract to a conference that’s coming up. It’s an internally run conference that the hospital puts on every year for us to share our work with other labs. A lot of the stuff we do in the hospital is similar across labs so doing stuff like this helps everyone explore different collaborations that could be done or work that compliments other work. There’s a few things that need to happen now that I’ve been selected and there’s not a lot of time to do it, but what else is new?

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The first glimpse!

woman standing on broken stairs leading up to sky in the distance
woman standing on broken stairs leading up to sky in the distance

Well I don’t want to say we have something… but we have something! Okay, so I guess we should back up a little bit. A few days ago we collected some data using an idea I had, my “big idea.” This was the first time we did this experiment the way I really wanted to do it, but not the first experiment, so we had a really good shot of getting some good data. Shortly after we finished the experiment I did some quick checks and we did, in fact, have data. Now the question was, what did it all mean?

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Data rush

Okay well I don’t know how successful our experiment was… yet. I know we have data, which was the first hurdle, but does that data tell us anything? Will we unlock the deepest secrets of the human body (almost certainly not, but we can dream), or will we just end up with a whole lot of nothing. That’s the problem with trying something for the first time, you could have something, or you could have nothing and it’s a lot of work before you find out the answer.

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Small beginnings

Tree seen at night, in the dark, with lots of stars in the background and light around the tree.

Sometimes big things have small beginnings. Honestly I’m not even sure how to talk about it vaguely, but I’m going to give it my best shot. The short version is that I officially have my first dataset for an idea I had almost a year ago now, a “big idea” as it were. I’m confident that this will work, I haven’t had a chance to see what we got, but I did make a few initial checks to ensure everything was collecting correctly. Unfortunately, despite how monumental this feels for me, I can’t explain what we have… yet.

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The third lecture!?

It’s time! Okay not quite, but very soon! It’s time for the last of my summer lectures for the interns and I’m excited to wrap this up and focus on other work. There’s a lot going on so maybe first we’ll talk about how my schedule conflict shaped up, what I’ll be teaching, and why I love this class so much. I’ve been debating about making a seperate post to share the knowledge. Since I did that last year, with the classes I’m teaching this year, I don’t know if it makes sense. Maybe a review would be in order anyway…

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A new grant proposal

Have I mentioned I like making work for myself? I mean, I really don’t I am a lazy person! I would prefer to do absolutely nothing, I swear, but for whatever reason, I keep making new work. As much as I love the stuff I do, this particular bit of work is my dream. And dreams cost money, so unfortunately because my dream has been unfunded, we haven’t had a chance to do anything with it. I mean we have, but not quite.

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Summer conference!

Add one more thing to my to-do list, but not in a bad way exactly. It’s summer time, which means it’s time for the annual summer conference we hold at work. This is an “internal” conference run by the hospital for all the students and summer interns we have. It’s fairly large and gives us all a chance to share our science and see what other labs are doing in the hospital. What’s nice is that this sometimes leads to really cool collaborations (we recently did one actually).

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Self-promotion in science

I admit it. I’m bad at promoting myself. It’s hard and I hate it. I’ve made a concerted effort to do just that though and over the past couple of years I think it’s helped, maybe? The problem is half of the metrics we use to measure success as a researcher come down to popularity. Things like h-index are great measures, but what they are measuring isn’t always how good your research is, more like how many people know your work. Which to be fair are similar, but still different things.

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DARPA Risers 2022

Well it’s even more official! I’ve been selected as a 2022 DARPA Riser and I’ve gotten more details on the event. Today I figure it’s a good time to talk about the process as I know it and where we are in that process. Mostly because the internet had very little on the topic and because I am very excited to be part of the selection. I also now can view my fellow DARPA Risers, which has been more than just a little humbling.

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Effects of transcutaneous spinal stimulation on spatiotemporal cortical activation patterns

The list of clusters of activation we found in the brain due to transcutaneous spinal stimulation (TSS)

It’s official! My latest paper, what I’ve been calling “last paper” is now typeset and I can share my fancy videos better. I’m excited that this is finally here and since I gave a good overview of the paper (here) today I’ll discuss a bit more about why this paper was important and why the dataset was such a pain, both of those I had to shorten due to the length of the post.

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A big breakthrough!

Okay I’m trying to remain calm because nothing is set in stone yet. However, I’m very excited because as of yesterday anyway we have the first person who is eligible for the experiment I proposed using what I call, “big idea.” Now for those of you who have been following along, this may be confusing because I already have several datasets using this new thing I’ve created, but this is a little different. Okay a lot different and I’ll explain why.

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Another response letter

There’s a surprise paper I haven’t talked about much. Mostly because I’m “only” second author on it, but also because as I keep mentioning things are hectic. However, we’re almost a full six months into the year and I currently have three papers (two first author, one second author) to my name and this will be number four! It’s been a good year for me, but we’re not done yet! Today I’m going to once again talk about response letters.

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Summer experiments

With summer here in pretty much full swing, we are about to get started on a bunch of new experiments. There’s a lot of things coming that will make life slightly harder, so in an effort to keep track of my progress between now and the big graduation day (soon… hopefully), let’s look at what I’ve got going on this summer. Things I need to do, things I “get” to do, and things that I can pawn off on others to do *wink.*

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The hard road

Is doing something an easier way necessarily worse than doing it a hard way? I mean with a lot of things in life you get out what you put in. If you work hard enough you could be an olympic athlete, a world class musician, dancer, artist. But even in those cases, is it hard work, or consistant work that makes the difference? I’m not sure one way or the other, but I’ve typically opted for the hard way. It’s lead to mixed results, but typically I don’t mind putting in the extra effort if it means that I will have a good outcome.

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Effects of transcutaneous spinal cord stimulation on the brain

Experimental setup (explained in detail below)

Transcutaneous spinal stimulation (TSS) is a relatively new approach to neuromodulation. We can activate networks in the spinal cord by injecting a small amount of current through the skin, which evokes a response in the muscles (muscle contraction). Depending on the person the electrical stimulus (the zappy time) feels either like a massage or it can be uncomfortable, not exactly painful, just not something you would go out of your way for. But the spinal cord is a two way street, so what does TSS do in the brain?

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More experimental prep

Is this our setup or is this electronic equipment from the late 50’s? I’ll never tell… (okay, let’s be real, this is a lot nicer looking than our cable mess).

Things have been busy, welcome to my life. But seriously, there is a lot happening right now, most of which is top secret (shhh don’t tell anyone). But as usual, leading up to an experiment, there’s a lot of prep work that needs to happen. Mostly because things always go wrong and we want to maximize our chances for them to go right. So let’s dive into what it’s like the second time.

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Success! Journal paper 4 of 4

I’ve been waiting for this day for years, but here we are. The fourth and final paper, what I’m calling “last paper” has been accepted for publication as of this morning! It’s been a long, hard journey and this paper didn’t make anything easier, but it’s almost over. It just needs to go to typesetting and that will be the last of last paper. As with the others, it’s time to look back and the journey last paper took and how I finally got here.

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Living through history

When I was a kid I thought history was something we read about in text books. World wars were from a “less civilized” time, we are a modern people after all. With the fall of the USSR along with the start and end of the gulf war not too long after, I thought, perhaps foolishly, that history was a thing of the past. I never suggested I was the smartest of children. But here we are, living through history. I didn’t realize it could be so painful, then again maybe if I had paid more attention I would’ve known.

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Data mountain

Well the week is over and I’ve barely been able to drag myself out of bed it’s been so exhausting. Unfortunately, we’re doing it all again next week too, so it’s not over yet. But the first of two test experiments are done, I say test because these don’t actually count toward our original set of experiments we’re doing later this summer. Meaning there’s going to be a lot of work coming my way, fun times.

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More on experimental prep

I kind of wish my equipment looked this cool…

Since we have a rather large and cumbersome set of experiments happening it’s my job to make sure they go off without too much trouble. I say too much trouble because no matter how much you plan, test, and retest, something will go wrong. Heck it may not even be wrong on our end, it may be wrong on someone else’s side, but that’s why we plan. So once again I’m talking about how we prep for our experiments.

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A big revision

Ever have a really good idea, maybe even a “big idea?” Well I’ve apparently had a few, but some are bigger than others and currently we’re diving into some very intense experiments using my “big idea,” but we’re running into certain limitations. While I could happily call it here, not put the effort into doing anything about it, and just live with it, that’s not happening. For anyone who knows me, that’s not even an option. So instead big idea is getting a big revision.

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Making greatness

I do love making… new friends.

If you build it, they will come? Okay not quite, but if you can buy it you need to make it. That seems to be the theme for the next few weeks as we’re getting ready to start several different experiments and the scope of them is massive. Not so much the experiments themselves, but everything that is going into them and everything we are going to get out of them.

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Adventures in experimental design

When did people start trusting me with experimental design? I have no idea, but here we are and I’m helping come up with a series of experiments we will be doing in roughly one week… seven days. So between now and then, we have a lot of things to figure out. We have a rough idea about what will happen, but there are a lot of moving parts and it turns out we are probably missing a few things so we’re going to have to get creative if we really want to get to the bottom of things… fun times for all!

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Whatever it takes

Well, yesterday happened. If you’ve been following around for awhile the last time I didn’t write a post we were dealing with apocalyptic weather (as in no power bad). So I think after years of being consistent, I wouldn’t blame you if you thought something bad had happened. In reality, there was just a mountain of work and no time to relax. I don’t like pushing myself like I had to yesterday, but it was for a good cause or at least I think so, or I wouldn’t have done it.

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The mysterious data

I sometimes miss the days when the answers were in the back of the book. At this point I would take even just having answers that are semi related to the questions I’m trying to work out. Being a researcher is a double edged sword. On one side, for a brief moment in history you will know something that no other person in the world knows. On the other, how do you know that it’s correct? Questioning your results is an important part of research and right now, there’s more questions than answers.

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Mounting pressure

After yesterday’s win, you would think things would be smooth sailing, but alas that isn’t in the cards! I mean yesterday’s good news still applies thankfully, but wow did I wake up to a flurry of emails and now a mountain of work that all needs to be addressed all at the same time. Wait, is there an echo in here? I feel like we’ve done this before…

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A big result

night scene showing young boy with a little moon in his hands sitting on meadow done digitally
night scene showing young boy with a little moon in his hands sitting on meadow done digitally

I’m stepping away from my planned sharing of the notes from my lecture to bring breaking news! For those who don’t understand what’s going on, a while ago I had an idea, a “big idea” that I’m convinced will be the thing I’m known for… if it works. And our first attempt was not great. In fact, we got absolutely nothing. The second and third attempts however we were ready and it looked like we had something. The question is what did we have?

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The first lecture

The thing is today?! What, how did that even happen? Yes, I know the linear nature of time, but wow does time have no meaning these days. What am I talking about you ask? Well today is my first lecture, hence the title of the post. Unfortunately I’m not exactly ready, but I am going to be recycling a lot of the stuff I used last year when I taught this class, so that shouldn’t be a huge problem…. or will it?

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From imagination to reality

It’s amazing what a good night of sleep will do for a person. Hopital-PI often has what he calls his “shower ideas” and frankly, my “big idea” was also a shower idea, but I find that the best ideas come to me when you’re not even thinking about them. When you step away from a problem and focus on something else, your brain just does something magical and works out the solution without you even realizing it, sometimes anyway.

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A dissertation dilemma

Okay, since I’m still waiting on my new and fancy toys to arrive for my dissertation I’ve been debating about going through the whole thing once again using the equipment I already have access to. Since there’s a limited amount of time I may just have to power through and go ahead with data collection using the old equipment, but it’s still anyone’s guess if I’ll do that because frankly I’m not sure it will be worth it. Since it’s up in the air, I figure I can write out my thought process and hopefully figure it out one way or the other.

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