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Posts tagged “neuroscience

Yet more papers!!

Well if it isn’t the week of every single thing that needs to be written needs to be done today, I don’t know what week it is. For those keeping score, I’ve successfully had one paper accepted for publication, had a random update and submitted a second paper for publication, and now I’m working on two other papers while I’m waiting to hear back about a third. What a week.

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It took multiple days to write a single paragraph and other odd, but true tales

Maybe I’m just weird. Okay, I’m definitely weird, but that’s not the point. It’s been three full years since I started my PhD and I’m still pretty self-conscious about idiosyncrasies, or at least the ones I’m aware of. Some of them aren’t a big issue, some of them may just be preferences, some of them just could be from the way I was raised. Whatever the reason, I thought it would be fun, or at least funny, to share some of the weird things I’ve done.

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The week ahead

There’s a lot happening this week, it SHOULD be the last week I’m technically jobless. Right now I’m not getting paid by anyone, not by the school, not by the hospital, basically I’m living off the last paycheck I got at the beginning of the month and the next one may not be here until close to the end of next month. If something happens and my start date gets pushed back, well that would mean that I would have no money for anything. That would be bad.

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The transition to clinical research

Today should be interesting… it’s my onboarding appointment, which is one of the last steps I need to complete to be hired at the hospital. There’s a lot going on in life at the moment, some of which is personal so I won’t be sharing that here, but let’s just say everything has been incredibly stressful. Oh and since I need to get the appointment done this week if I want to start on time, this was the last day I can get it done.

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PhD proposal prep

Well I’ve finally made it to the next milestone in my PhD. I’m now at the point where I can do my proposal defense. It shouldn’t be too bad, but there’s a lot involved between now and then that needs to happen including coming to some sort of an agreement between my two PI’s about what exactly the project will consist of. Since I had no idea what getting a PhD entailed when I started, I’m assuming at least some of you have no idea what’s going on so let’s go over how we got here and what I’m getting ready to do.

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Success! Journal paper 1 of 4

Psst, hey you! I got good news! I’ve officially had my first journal paper accepted for publication! I’m literally crying I’m so happy right now. My inbox has been flooded by emails from my collaborators congratulating everyone on this. It’s been a long, hard, and often painful journey, but I’ve finally, FINALLY, gotten something finished once and for all. Since this is the end of the story, let’s tell it from the beginning, one last time, so you know how we got here.

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The plastic spinal cord

Amazing spinal cord slice artwork by Greg Dunn

You can’t teach an old spinal cord new tricks, or something like that. Up until recently (like the last ten or fifteen years), we had thought that the spinal cord was a fixed thing. It was the information highway of the body and its primary role was to receive, sort, and send information from the brain to the body and vice versa. That’s (thankfully) not the case. The truth, or at least something closer to the truth, is that the spinal cord is a lot like the brain. It can learn, think, and even act independently of the brain.

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I wanted to be a scientist

What did five-year-old you want to be when you grew up? I see this question pop up on twitter every so often, or rather the question is often would five-year old you be proud of where you are now. I think it’s hard to judge your five-year-old self when you’re an adult because the world looks a whole lot less polished and magical when you’re an adult. In my experience as you transition to an adult that magic and wonder is slowly replaced with dread, anxiety, and mostly doubt. Imposter syndrome is a real thing that many people, including myself, deal with.

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The art in science

One of the easiest ways to turn even the most advanced scientific paper into something accessible is through carefully crafted figure design. Figures are a way to tell a story, but to also capture the readers imagination. The difference between a scientific figure and a drawing from a story is really just the difference in the information you are conveying. However, as is the case with most things in the world, a “good” figure is in the eye of the beholder.

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On trying something new

As a grad student the work/life balance tends to blur. I actually do most of my work on the weekends and tend to try to take time during the week for myself. This works best for me because weekends are typically when no one needs me to physically be somewhere, so I can get into the correct headspace to do some work. This weekend was a busy one, and my Co-PI had some ideas about one of the papers I’m working on that required my full attention. He also wants me to do something I’ve never done before, so let’s talk about trying something new!

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Non-invasive study of the brain

Art by the incredible Greg Dunn (I REALLY!!! wish I could afford his work!)

Non-invasive research is difficult, especially when you’re working with something as complicated as the brain. Imagine being at a pro sports game outside the stadium and trying to figure out what’s going on inside just by listening. I’m constantly in awe that we can record activity from the brain without breaking the skin, it’s like magic. However, it’s still difficult and not without controversy.

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The uncertain future

old door in middle of field, which opens to a whole different world.
old door in middle of field, which opens to a whole different world.

My Co-PI is leaving! Or maybe he’s not? But he could be?! I don’t even know. It doesn’t help that he has no idea and there’s no real deadline for him to make a choice, it’s whenever he’s ready. In fact, we currently have a line graph with his daily percentage on staying or leaving. I wish I was joking. It’s not just my future I’m worried about, there are others in the lab, most of us wouldn’t be able to make the journey to his new workspace, even if we wanted to (and trust me when I say if I could, I would).

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A small success

It was a leap of faith. There were no good choices, but it was the best of options in a string of bad options. I could either work full time in my main-PI’s lab, pulling me away from the clinical research I love, or I could take a job in my Co-PI’s lab. The catch was to take the job with my Co-PI I would have to apply, wait, and go through the onboarding process. That would mean I wouldn’t be getting paid, which would be okay for a few weeks, but longer and I could be in trouble. Nothing is finished yet, but I’ve gotten some good news.

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Minor revisions

Ah, just when I thought I didn’t have to worry about one of the multitudes of papers that I’m working on, it comes right back. This is the journal paper I wrote for one of my classes, which looks to be about ready for acceptance. There were some minor revisions that we were asked to make, but as of ten minutes or so ago I’ve addressed all of them. I think… it will probably be another round of edits with our co-authors to make sure everyone is happy with what we’ve done. Maybe? I’m not even sure at this point.

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Sometimes it rains

Brains are wild. I mean we have this misshapen jello blob stuck in our head and it somehow gives us the ability to be aware. We exist and think, feel, reason, all the stuff that makes us who we are. Brains are great, except when they aren’t. Depression is a horrible thing, which lives in the brain. You can’t “just be happy” anymore than someone could just be rich. Obviously when you live with chronic depression you got a dud of a brain. It may have to do with genetics, environmental factors, the way we were raised, or maybe it’s just horrible luck, but out of all the organs we can fix or replace, the brain is not one of them. You’re stuck as you and sometimes that sucks.

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Controlled chaos

Life has been pretty messy lately. Not just because of the pandemic, but that is definitely not helping anything right now. I’ve got papers due, I’m making a job change, and the wildest part is that my Co-PI may be leaving so I’m not even sure the job I’m changing to will still be there after the end of the year. That doesn’t include the outside factors, car issues, home issues, health issues. Those are all there too, but mostly right now I’m concerned about work related stuff and I realized that for the past few months it’s just been controlled chaos.

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Multi-paper madness!

HELLLP! I’m doing way too much writing and it’s the scientific kind, which is to say soul sucking! Okay, it’s not that bad, but for the past month it’s been a mad rush to get several different papers written. Today I plan to go over all the papers I’m working on, the progress I’ve made, and why I really hope I’ll never have this happen again. Far too much writing! It has to end eventually though, right?

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The R21 Result

Well I’ve been meaning to write this for a bit now, but the R21 I helped write back at the beginning of the year was not funded. It was a longshot and my Co-PI who helped write and submit the proposal was not surprised as to the result. Worse, it was not discussed. Since I’ve spent the past year learning the hard way how grant writing works, I figure today I can pass on that knowledge and we can who knows, maybe it will help others who are grant writing.

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Countdown to the grant submission

We’re just days away from the deadline for the grant I’m writing. We’ve got an awesome team of people that have agreed to be a part of this project and the funding will go towards the big idea I had several years back (what I’m calling my “super secret technique”) so I’m excited! My main-PI thinks the proposal has a good chance of being funded and I trust his judgement since he’s been doing this for a long time. So today I figure I can brag about the team and what will happen in the next few days.

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An unfortunate typoo

Yes, the title was on purpose. No, I’m not thrilled at the moment. Sometimes you just need things to go smoothly, but life has other plans and yesterday I hit one hell of a stumbling block. The good news is I’ve caught it, but the bad news is there is now about 104833423x more work for me to do to fix the issue. No matter how careful you are, something is always going to get missed, yesterday was just a reminder that you can miss things even when you’re paying close attention. I may go as far as to say, especially when you’re paying close attention.

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Why is it always a rush?

Well my latest grant is due at the end of the week, so I am now just a few short days away from the deadline and rushing to meet it. There has been plenty of time between when the proposal for funding went out and now, so why does it always feel like things are last minute? It probably has to do with the iterative approach to writing and the edits that go on forever. Since I need a break from scientific writing I figure now would be a good time to talk about the process and why a far off deadline is never enough.

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The final day of summer internship

Today marks the last day of the summer internship for our early career undergrad researchers. On paper, it’s been a long, sometimes bumpy road that wasn’t always the easiest thing to work through. In reality, it was all too short and it feels like we just got to know our interns and now it’s time to say goodbye. Through the experience I’ve got to watch the intern I was mentoring grow as a person, and grow more confident in herself. It’s been a privilege that I got to be a part of this.

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The hunt for knowledge

Sometimes science is like digital archeology. Thanks to the internet I have the sum of our collective knowledge at the tips of my fingers. I just need to ask the right question and I can find the answer. Unfortunately, the right question isn’t always the question you come up with. The right question may not be worded the exact way you think it should. The right question may not even be the right question at all, it’s just the first in a long list of questions you need to work through. In a digital world, we’re still stuck looking for ways to get the answers to questions the system may not understand. I’m on a hunt and so far I’ve been fairly lucky.

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Juggling papers

It finally happened, it’s the big deadline, or at least most of the stuff I have due is due pretty much right now. I’ve been working on three different papers, and now I have a fourth added to the mix that I sort of forgot about until my Co-PI asked me to review the work we did in that paper, so yeah a lot going on at the moment and it’s all basically writing. So of course I’m working hard on writing… this. The truth is I need a break so I figure blogging would be a good distraction while still feeling like I’ve accomplished something. It beats doom scrolling twitter until the entire day has passed me by.

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Nothing like the first time

There’s nothing like your first time. The first time you accomplish something is new and exciting. Feelings that are hard to capture a second time, much less repeatedly. It’s a magical experience, especially when the first time is good and can be a powerful memory to hold on to no matter how badly things go. When it comes to presentations, in my opinion, everytime is the first time and that can be a point of nervous energy for a lot of people. Next week is presentation time for the summer interns, for their the first time, ever.

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The complexity of biology

Why couldn’t things be simple? Maybe you would take a measurement and have the correct value every time. Or you would perform an experiment and get the same result no matter what. The human body is an amazing feat of engineering by evolution. It’s layer upon layer of stuff that all work together to do the thing that needs to happen. The fact that it works at all is amazing, it’s like throwing a bunch of computers into a room, shaking it, and out comes a fully working robot that’s more advanced than anything you’ve seen.

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The big presentation

It has been a day friends. Yesterday I got an email from my main-PI asking me about a funding proposal I’ve been working on and when I responded I asked if we were having our lab meeting this week since the last two have been cancelled. He said yes and he mentioned that today would be the day I presented the work I’ve been doing with my project. Thankfully I was ready for it, but it was pretty stressful and there are some changes that need to be made. Overall the lab seemed pretty impressed by the presentation and the work I’ve been doing.

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The value of planning your code

It’s no secret I need to write code, a lot of code. A mind numbingly large amount of code. Researching in a brain-machine interface lab is more about programming than it is about scifi brain hacking or anything the latest techno-thriller movies would have you believe. Anyone can do it, but it takes a certain amount of practice and a whole heck of a lot of time. Over time your skills develop and things get to be easier, but it’s not a linear progression (is anything really?) so things can be frustrating. These days planning saves me tons of time and effort, so today I want to pass that bit of knowledge on to you.

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Programming overreach

This is what happens when I try to get fancy with the work I’m doing. I end up attempting to do things that aren’t done easily or if they are done easily, I figure out the hardest way possible for me to get them done. A week or so ago (here) I was excited because I came up with a super cool way to do something and I thought that the hardest part was behind me. Oh how wrong I was… but I’m close to figuring this out, I just need to do a lot of work to dig out of this hole I threw myself into. This is why you should never do anything fancy!

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Sometimes the progress is slow

Today has been incredibly busy, but incredibly frustrating. So far next to nothing has been accomplished towards the work I have to do, but I did help a few people out and we discovered some interesting issues with some software the lab uses. Okay not issues exactly, it just doesn’t work the way we thought it did. In any case, there has been a lot of running around and doing things, just nothing productive for myself. Some days are like that though, hopefully I will have better luck tomorrow or maybe even later tonight.

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More competing projects

Were does the time go?! I have no time left to get my projects done and yet there’s still a lot that needs to happen. Today is one of my semi-famous lists of stuff I need to get done in an outrageously short amount of time. Didn’t we just do this a month or so ago? I think so, but here we are counting down yet again to the newest set of deadlines and as with all my deadlines they clumped together and fall at what amounts to the same time. Don’t believe me? Well let’s take a closer look.

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A unique figure design

Over the past few weeks I’ve been hard a work making a new visualization for some of the data I’d recently processed. This again is for the project I won an award for (here), and while I’m not trying to brag, I’m super proud of how it came together. It was the first time I tried to do something like this and not only did my main-PI give me his approval it sounds like a lot of people from the lab were impressed with this as well. Unfortunately, I can’t quite give away what I did or how I did it, but I can share some of this.

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Initial results!

Okay I’m excited! I had a project my Co-PI offered me for the summer that I really, REALLY wanted to do (this one). We’ve been slowly collecting data and haven’t had a chance to do a detailed analysis of the result yet. It looked like we had something cool, but we weren’t sure what it was. Our data had a lot of noise in it (which is a given when working with EEG) and we needed to clean it to give us a better “view” of what was going on, so yesterday I sat down to do just that…

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Conferences in a pandemic

I’m vaccinated, I got vaccinated back before most of the public could because I work and do research at a hospital. Because I work with a vulnerable population, some of whom cannot be vaccinated, I still take the pandemic very seriously. I wear my mask like I wear any other piece of clothing and the hospital understands this risk because unlike schools and other places in the area, masks are still mandatory. It’s not just a vaccination issue, it’s that vaccines are 100% effective and not everyone can be vaccinated or has access to get vaccinated. So when my favorite conference came around, I was torn about attending… was.

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Working in higher dimensions

Imagine if you will, only being able to move along a straight line. You’re now in one dimensional space. But wait! What if we are allowed, quite literally, to take a left. You are now allowed to move along a square space, this is two dimensional space. We can do better, though. You suddenly can move up and down, traveling in an area that’s the shape of a cube! You’re now in 3D space. Then suddenly you disappear from view, but where did you go? Welcome to the fourth dimension, you can’t see it, you can’t imagine it, but we can do math here and above!

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Finishing a project… maybe

Today is the day! Well, maybe today is the day, I’m hopeful though so let’s go with that. Today is the day I finish the analysis of the data I collected a while back for the experiment I wasn’t super thrilled about doing. The one I got an award for doing, funny enough (more). This project was a huge headache from the start, but I’m finally about to do the last bit of the work on the analysis and then all I have to do is write the paper. So let’s talk about what’s going on.

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Experimental limits

Well this is turning into a drama, but we keep having issues with the experiment. There are once again changes that need to be made, we’re four out of ten planned experiments into the project and while we’ve done the first four the same way, we keep trying to adjust our testing to a slightly different version of the protocol and it’s running into… issues to say the least. There are some things we just can’t accomplish using our testing paradigm and we have to accept that, but we still try to push those limits, even if it hurts.

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Technical problems

While people worried about the robot apocalypse, I’m not. If I need to randomly turn my router off and back on again for it to work properly I doubt Skynet will somehow gain sentience and take over the world without someone needing to go in and reboot it from time to time. Technology is an imperfect thing, like biology, but we expect technology to be better than us at what we need it to do. Today we spent almost an hour doing a little dance with the technology in the lab trying to get all the pieces to play nicely. The robot apocalypse will be short lived.

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We meet again, figure 1

If you’re new around here, I’m working on a handful of papers all at the same time. Five in total, all first author journal papers. For those not in academia, that’s a lot. I don’t know how this happened or why it happened, but here we are. Two of them are basically finished, two are just starting, and one will (hopefully) be started soon. Which brings me to the topic of the day, figure 1. Figure 1 is arguably one of the most important figures in the type of work I do, so let’s dive into why and what I’m trying to accomplish.

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Sometimes you’re too close to the problem

I’ve had a breakthrough! I’ve been working for months on a problem and I probably could’ve come up with the solution sooner if I hadn’t been trying to force it. Maybe I’m weird, but I find the easiest way to come up with a solution to a problem is to just walk away from it. I don’t always do it, but I always end up regretting that I didn’t just step away from the thing long enough to get the full picture.

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The connections we make

Networking. It’s all we ever hear about. It’s not what you know, it’s who you know. Maybe it’s not even so much about who you know, but how you approach people. I know if it were not for the people I’ve reached out to, I would not be where I am today. In fact, I can think of at least a handful of people whom I’ve reached out to only to have them change the course of my life for the better. Yesterday I got the chance to do the same for someone else.

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Two wild days!

If you’re reading this then it’s too late for me. Or rather it’s too early for me since I need to be up super early tomorrow, which is today (when you are reading this). Confused? Well it’s supposed to be a daily blog of my progress, but I’m cheating and writing today’s post last night. That’s because really, if you’re reading this I’m in an experiment. No, it doesn’t matter when you read this as long as it’s the day I posted because I’m definitely in an experiment. Don’t worry, I’ll explain.

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Experiment result preview

This summer I am performing an experiment that could change our understanding of what a certain type of stimulation is doing. It’s all incredibly exciting (as always when I’m in my Co-PI’s lab) and I get to be the first author on the result. If we can show that this thing we are looking for is true then it will be a big shift in our understanding, but more importantly it will open the door to new types of non-invasive treatments. While I cannot talk about the details (as always) I can share that I’m excited about what may be coming.

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The week ahead

For a few weeks I was trying something new and doing a “week in review” well this week is exciting for a lot of reasons so I wanted to look at the week ahead! As usual I cannot give details about what is going to happen or why, but at least I can share my excitement and maybe one day soon I’ll be able to share what we did and point back to this post. So instead of looking back, today we’re looking forward. It’s going to be busy, but hey what else is new?

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When a good experiment goes bad

I love stock photos, this is just too funny to me. Plus it’s how I feel most days.

Weeks of planning. Thoughtful discussion about the variables. Finding the perfect way to set things up. We ran tests, we collected pilot data, everything was ready, or so we thought! The thing about running an experiment is that you never know what will happen, especially when it’s the first time you’re doing it. Even though we tested the equipment independently it wasn’t until we were doing the actual experiment that the problem immerged. Never fear though, the story has a happy ending.

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Start of summer experiments

Well today is the day! I’m just hours away from collecting my first dataset for my summer project. I’m excited, it’s a cool project and I get to be first author on the paper. The topic is impressive to me so I think it will be a good way to get my name out there in the field since this will be my first paper in my Co-PI’s lab (well first, first author paper). It’s a lot of responsibility and of course I don’t have any time to prep. The first experiment is always the hardest…

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Learning is sneaky

Three years ago this fall I walked into my main-PI’s lab for the first time and I knew nothing about the work we did. I was a mechanical engineer and had machining, solid modeling, and control experience. None of which helped me in my new position. Learning something new is a slow process. The more you learn the more you realize you don’t know anything and it feels like three years later I’m just as clueless as I was when I first set foot into the building. Learning is sneaky that way, you don’t always realize how far you’ve come.

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The start of a busy week

Splitting your time between two labs should be pretty straightforward, on one hand my two PI’s have come to an agreement about how my time should be split and in a 40 hour work week, each should get roughly 20 hours of my time dedicated to the things they are working on. Easy, except it isn’t. Both are used to 40 hours to their lab and I’m not complaining, I enjoy being wanted, but as my Co-PI pointed out I have a lot going on and I need a break. Literally he told me to take a break, it’s bad enough that my Co-PI is telling me to go home.

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My talk is today and you’re all invited!

Okay so I wanted to update everyone on how my first lecture went yesterday since I only had a few short days to throw everything together and it was a mad panic to the end. Unfortunately we cannot go into detail today! That’s because today is my “I’m giving a talk” talk (which I wrote about here). It’s free to watch, my talk is roughly four minutes long and is a nice little rundown of some of the work I do. So today I figure I will go into a bit of detail and should you be so inclined to attend you’ll get the chance to chat with me in person about my work! Yep, I’m breaking anonymity yet again, but it’s for a good reason.

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Depression, a tale of hunger

Let’s pretend you have a pet that is constantly hungry. You can’t leave the house, you can’t sleep, you can’t even take a shower because anytime you want to do something for yourself this monster of a pet just won’t allow it to happen. It’s hungry. It wants to be fed and it wants to be fed NOW. Oh you’re exhausted, feed it. You want to do something for yourself? Too bad, feed it. It’s all consuming, it never sleeps, it never is satisfied, and you cannot get rid of it. Chronic depression is the pet you never asked for that demands your attention all day, every day.

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