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Posts tagged “science

Day #162: Know your spinal cord – The spinothalamic tract

Antique engraving illustration: Spinal cord and brain

Day six already! Today is day six of knowing your spinal cord and we’re talking about the spinothalamic tract today. If you’re interested in the other posts, the first covers the medullary pyramids and I even have a category just for these posts. Of all the tracts of the spinal cord, this is probably my favorite becuase it is just so weird! You’ll see what I mean, so let’s get to it.

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Day #161: Know your spinal cord – The medial lemniscus tract

spinal drawing

Here we are day five of knowing your spinal cord. If you’re just joining us, I’ve created a new category where you can find all the posts. Or you can start at the beginning with the medullary pyramids (technically not part of the spine, but close enough). If you’re all caught up or just want to learn about this specific tract, then let’s get started.

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Day #160: Know your spinal cord – The corticospinal pathway

spinal cord cross section drawing

We’ve made it to day four of knowing your spinal cord. I’ve introduced a new category just for this, which makes these posts easier to find for future reference (yours or mine). For those of you just starting out, you may want to go from the first post on the medullary pyramids. For the rest of you, you’re probably here to learn about the corticospinal pathway. This will be fun, so let’s get started.

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Day #159: Know your spinal cord – Organization

spinal cord

For those of us just tuning in, today is the third part in a … well a lot of posts on the spinal cord! If you’re just joining us, you should probably start from the top (literally) here and this post covers the anatomy of the cord. Today we are going to talk spinal organization, for that reason we also should talk about how the brain is organized, which will help us make sense of why the spinal cord is organized the way it is, so let’s get started!

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Day #158: Know your spinal cord – The anatomy

leonardo da vinci spine drawing

Now that we took it from the top, let’s get an overview of what exactly makes up the spinal cord. There is a lot, so we’re not going to do a comprehensive review since that would be a whole class and not a single post. Most of the structures we cover today, will have a seperate post where we can go into detail.

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Day #157: Know your spinal cord – Medullary Pyramids

brainstem drawing

I’m excited that today we are starting the know your spinal cord series that I’ve been working on. Today we are going to take it from the top, no really. We’re starting at the top of the cord and we will work our way down. So without further delay, let’s look at the curious case of the medullary pyramids!

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Day #156: Experiment results

cervical spine

Well to say it’s been a busy week is probably an understatement and it doesn’t seem like it will be slowing down anytime soon. As it stands today was the end of our data collection. We managed to get ~15 subjects to go through our protocol and while I cannot share anything (yet) I can talk about the stuff I’ve learned and what is coming.

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Day #155: Experiments!!

So it turns out when you have 12 hours of experiments to do there isn’t much time for other things. Yesterday we had 3 experiments, today we have another 3 experiments (technically I’m writing this yesterday night, confusing I know). So basically I don’t have a whole lot of time to write. I’m going off to get some sleep and tomorrow (today, again confusing I know) I get to do this all over again. I hope wednesday I will have a bit more time and we can get into why the spinal cord is so cool! In any case, stay tuned!


Day #124: On the importance of time off

Overworked

When I left the military, I threw myself into work. I was offered — and I took — all the overtime I could get. If I stayed busy, I didn’t have to think about anything else and at the time, it is what I wanted. I didn’t want to have to think about anything else. It was an unhealthy and unsustainable lifestyle, one I don’t necessarily regret, just one I had to learn from.

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Day #123: Well I HAD a meeting

timeobsessed

Today I reluctantly had two things to do on my list, this despite being sick. Now, I don’t normally like going out when I’m unwell, I don’t want to get others sick, I don’t want to suffer more, blah blah blah. The usual things you’re supposed to do when you are sick. Well today I was not that lucky, let’s talk about why.

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Day #122: Moving forward

prosthetic head

After the events of the past week, I need a break. Not just because of all the excitement that has occured, but because I am sick. Like bad. There is never a good time to be sick per say, but if I had to be sick, this was about as good of timing as I could ask for. Let’s talk about what’s next once I’m feeling better.

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Day #121: Qualifying Exam Aftermath

Steele - QE

I don’t normally share photos of myself, but I thought I would share the final slide, I love it so much.

Well if you don’t follow me on twitter, then you don’t know the results of my qualifying exam. Well I’ll tell you, but not yet. First let’s talk about how it went and what the qualifying exam is (I know we’ve covered this already here, but it would be good to do it again).

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Day #120: The art of the data request (update)

RFI, Request for Information

Today is the big day, it’s my qualifier day. Since it hasn’t happened yet I cannot tell you how it went, but I feel pretty good about it. However, I still have a lot of other news to share, like my data request update. So let’s get to it.

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Day #119: Conference Day 4

Winners

The winners of the pitch competition giving a surprise 1-2 minute elevator pitch

Well, I’m finally home. It’s been exhausting, but super exciting. I’ve got so much to share I’m not even sure where to start. Let’s go over how yesterday went first. It was our last day at the confrence and our trainees got to present their company pitches. We named the top three (of ten) teams and they got prizes (surprisingly useful and super nice prizes, a wireless phone charger in fact). We also had some talks, so let’s go through the highlights.

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Day 118: Conference Day 3

It’s been a busy conference. Yesterday was a particularly full day and so today, I’m blogging via phone. This morning we hiked a mountain. Well A-mountain (seriously that’s the name of it).

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Day #117: Conference Day 2

Start

Today is the first day of the neurotech workshop (day 2 of my confrence schedule since I had 2 conferences back to back) and man did I do something evil. Well… maybe not that evil, but more evil genius. They gave me some creative power and I found a way to make it funny. Let’s take a look at the result, shall we?

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Day #116: Conference Day 1

moon view

Shot I took of the moon

Made it in one piece to my destination! Since I’m writing this before today’s events start, let’s talk about yesterday. While the bulk of the time was spent traveling it wouldn’t hurt to muse on a few of the events, especially since today will be a much busier (or at least more event packed) day.

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Day #115: Conference time!

airplane-travel

Well today is the day, I’m packed and ready for the … festivities? Okay, so maybe not something that is a party, but conferences are a good chance to meet with people and share ideas. While this is a small one for our research group, it’s still a way to let others know what advancements have been made in the field.

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Day #114: Classifier Update

NARXNET Classifier-Raw out

Behold! My amazing predictive power!! *insert evil laugh here*

It’s been a long and exhaustive road to get to here. As you may recall, I’ve given several updates already on my progress and I THINK I’ve finally hit success. In fact, I know I have, the problem now? Well what the neural net saw to make the predictions is a mystery to me, so I don’t know why or how it works… yet.

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Day #113:Practice makes… better?

Presentation practice

Conference is coming! With my talk right around the corner today is prep day. Basically I’m giving my talk today to the lab in the hopes that when I do it for real, it doesn’t completely suck. So practice, practice, practice!

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Day #112: Conference Prep

conference

We are just a few days away from my first of two events back to back. First up is the confrence I keep mentioning. It’s a meeting with collaborators from several schools to discuss work we’ve been doing that the group funded. I have one of those projects, so I will be presenting a powerpoint with an update on the work along with a poster that I’ve made.

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Day #111: A prosthetic update

colored-head.jpg

Prosthetic I’ve designed for Lucas, you can see the full view further into the post.

Now that the term is over, you would think I get some time to myself. That is unfortunately not true. There is still quite a bit of work ahead for me before I can take some time over the winter break to relax. One of the more important things that needs to happen is the prosthetic project I’ve been working on for some time.

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Day #110: Experiment!

EEG setup

This is an actual photo from my experiment setup, one of my colleagues is adding gel to the sensors. While the giant syringe looks scary, it isn’t. It’s full of conductive gel that gets placed between the head and the sensor. There is no pain or puncturing of the skin involved. Afterwards the gel washes out of the hair. The real pain is sitting for ~30 minutes or so while we gel each electrode enough to get a good reading.

A few days ago I mentioned I did a thing, well an experimental thing really. It was… fun? It was definitely something. Overall it went well, but I said I would give everyone an update and I try to be a man of my word, so let’s do this.

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Day #109: Post exam exhaustion

exhausted student.jpg

It’s over. The term has finally come to an end and I’ve taken my final as of yesterday. It’s bittersweet, on one hand I can now (sort of) relax. On the other, it means that there are exactly zero chances for me to improve my grade. I’ve done my best and now I need to hope that it is enough to get me to the finish line.

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Day #108: Final today!

exams

Well today is the day, finals! Well the only final I have this term really. I’m keeping my fingers crossed, but as you may have noticed from yesterday’s post, I’m a little stressed out… to say the least. So what’s happening today?

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Day #107: It’s an old friend

drowning being pulled underwater by dark tentacles

drowning being pulled underwater by dark tentacles

TW: Suicidal ideation
I’m having a hard time at the moment. It’s been building and I think it would be a good idea to talk about it before it gets bad. If you aren’t in a good headspace to read this, then you should probably turn away now. Otherwise, let’s get to it.

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Day #106: Super Busy!!!!!

Today I had my experiment (yay), so now I need to process the data. I also sat in another PhD defense for one of our lab members, so now that I have a free second I wanted to give an update. Expect a longer post tomorrow, but for today, I have sooooo much work to do!

Until next time, don’t stop learning!


Day #105: Defense day #1

phd defense

This basically sums up today’s post…

Here we are another day another post. Today I will be spending the bulk of my time studying and getting my slides ready for the confrence I’ll be attending next week. That will be … fun? However today is also an important day for one of my fellow students, he’s defending his PhD.

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Day #104: Experiment Prep

EEG headset

It looks like things are moving a little quicker than I thought for me. As you may or may not know, I’m getting ready to do an experiment. Well, we finally (finally!) finalized the protocol and just in time too. While I won’t make the deadline for my project update, I will have some data to show when we get to the conference, which is a good consolation prize.

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Day #103: A day off…

relaxing

I’ve got a lot going on, but today is a day off. It’s important to take time for yourself so when you need to do the work, you actually do the work. I’m sure we’ve all felt that way, where you force yourself to do something and spend 4+ hours doing something that you could do in less than an hour. Sometimes you need a break.

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Day #102: Finals ahead!

Warning sign

Well it’s that time of year again, finals! On one hand I’m excited at the prospect of being done with the term, on the other I’m a notoriously bad test taker. I deal with a lot of anxiety you see and even when I know how to solve the problem, come test day I end up drawing a blank or making very stupid mistakes. Standardized tests are the bane of my existence!!

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Day #101: Holiday

Well today is thanksgiving, not a holiday I celebrate, but I’m happy to have the day off at least. I’ll be taking the day to get some work done and relax some. Deadlines are coming so I can’t take the whole day to myself, but at least it’s a low stress day.

Until next time, don’t stop learning!


Day #100: Graduating lab members

Day 100 - PhD defense offense

Image from: xkcd.com

Wow, time flies, we’re already on day 100. Still not half way done, but it certainly doesn’t feel like 100 days of writing. Today has been a busy day, which is why I’m writing so late. With the end of the term comes other projects that need to be addressed, namely my qualifying exam, final exams, and other lab members having their Ph.D defense. Yep, we have not one, not two, but three people defending their Ph.D this term.

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Day #99: Data request, a update

letters vs email

Sometimes emails can still be exciting!

I’ve got news! In my last post on the subject I said that I wasn’t expecting a response from the lab I was requesting data from until Monday, if at all. Well would you believe I got a response! It wasn’t a “here’s the data response,” but it is progress. Let me explain why.

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Day #98: Laptop troubles

Well it finally happened. My laptop looks pretty dead. Right now I have it in pieces while I try to figure out what went wrong with it. Thankfully I have a desktop computer that I use for all my heavy computing as a back up. Just one more expense I guess, I should be grateful that it wasn’t something more serious like the hard drive going out.

So short post, I know, but I have to get this fixed or find some sort of resolution since my laptop is an important part of how I get work done. I’ll have a longer post tomorrow, but for now I think that is it.

Until next time, don’t stop learning!


Day #97: Neural network models

Neural net

Today should be an interesting day for me. I plan to do a deep dive into the world of neural networks to better understand how they work and the best type to apply to my data. There are a few, quite a few in fact that I could use and really it depends on how I want to frame my problem, so let’s look at what I’ve got planned.

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Day #96: The art of requesting data

Day 96 - mice

I have some data. This shouldn’t be news, I’ve been talking about how I’m trying to train a model to predict an output using this data and all the woes that have come from the training process. Turns out I have a problem, well more like questions that need answers and for that I need help.

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Day #95: Housework day

Pokemon procrastination

 

Pokemon procrastination

If only it was super effective!!!!!!

So far things have been non-stop and today is no exception. I have a lot of housework to do and balancing that work with my school work (all while still trying to find time to relax some) is difficult. Nevertheless today is housework day (mostly).

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Day #94: Paper formatting

submtting a paper

Ugh!! After over six weeks my paper was rejected becuase it didn’t fall in line with what the editor wanted. This is frustrating because each journal has different formatting requirements and you cannot submit to multiple journals at once so we need to sit and wait.

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Day #93: QE date is set… again!

5 tacks on a single date on a calendar

5 tacks on a single date on a calendar

Exciting news!!!!! Well as you can tell from the title, my qualifying exam date is set. After some time emailing back and forth I finally just sent out a doodle poll to get everyone to vote on what time would work best for them. Last night, my last committee member added their availability to the poll and with that, I have a new time and date!

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Day #92: Missed meetings…

65874759

As you may be aware, I am planning an experiment! Cue upbeat music Unfortunately record scratch I’m nowhere near ready. It’s been a process for sure and we are (maybe?) back on track to get started soon. Today I had a meeting scheduled with my PI to discuss the details, but…

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Day #91: Did that really just happen?

windows10 update screen

Screw you auto update

For those of you following along, I’ve been trying to crack a predictive model using some novel (read: super secret PhD work) neural data. It’s been a journey and I’ve trained and tested about a dozen or so models, with varying success. Things have been flying pretty smooth the past few weeks as I try to create the best model I could possibly create. Unfortunately, technology had other plans for me.

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Day #90: Memory

memorization

I have a lot of memorization to do these days. Things that are important , steps to set things up, new biology, new techniques, new, new, new… well you get the point. Memorization is the bain of my existence. It’s not even a matter of not wanting to memorize something, it’s just old war wounds, no really.

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Day #89: The stress of life

stress

Today I get to play catch up. I’m running on not a lot of sleep, but there is so much to be done it isn’t funny. Ironically enough, it’s not all school either. I have life things catching up with me, car repairs that I need to do, house things, you know the usual day to day things that pile up despite our best efforts.

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Day #88: Experimental Headaches

EEG

EEG cap

I’ve talked about my impending deadlines a lot lately. I also mentioned that I had an experiment that I needed to do to meet a deadline, well it looks like we may or may not meet this goal. Let’s talk about the latest headaches.

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Day #87: Classifier progress

Kernal function

Well it’s been an interesting experience. I’ve been working hard to train a binary classifier to predict the two classes in my data. There has been a lot of ups and downs and more importantly, there has been some progress. It isn’t perfect, but it’s a start, so let’s look at what I’ve got so far and where I’m headed.

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Day #86: Or maybe not…

vicous cat

Even my cat doesn’t like the news.

Last post I had triumphantly declared that I had scheduled my QE date…. wellllllll maybe not. I had a last minute email from one of my committee members saying they had another obligation that day that they had forgotten about. So today let’s talk about why that is okay, even though it isn’t really.

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Day #85: My QE date is set

Brain

Sometimes you need to get… a head. See what I did there?

Well it happened, the date for my qualifying exam has been set. I’m nervous, I’m excited, I’m mostly just anxious to get it done. Quite frankly I’m exhausted, so it will be nice to get one thing off my to-do list. Let’s look at how I need to get ready.

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Day #84: Model training progress

 

Day 84 - SVM hyperplane

Two dimensional data is easier to visualize than 202 dimensional data.

I don’t normally leave my computer on 24 hours a day, but it has been hard a work, so it hasn’t been off in days. Training a model can take some time, as I am finding out and while I’ve made progress on the resulting model, it’s still not where I want it. Let’s talk about what has been going on.

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Day #83: An unexpected gift

Day 83 - Gift

I’ll let you in on a secret, I’ve been doing science outreach on a regular basis for the past 3-4 years now. Specifically with Skype a scientist I’ve volunteered every term since it was pretty much first started. My secret, if not horribly kept, is this… I am ALWAYS nervous to give my talk. That doesn’t mean it isn’t worth it and let me explain why.

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