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How to Get Reeled into NeuroDuino – a Mathematician’s Guide (Part II)

Neuroduino
A NeuroDuino, Backyard Brains’ latest prototype

Hi there, it’s Natalia Díaz again with an update to my neuromathematical (yes, such a thing exists!) project. If you don’t remember me, I’m a student of Mathematical Engineering at the University of Santiago de Chile and I’m doing my internship here in BackyardBrains.

Since the last time we met (you and I, that is), BYB co-founder Tim Marzullo sent me some cool stuff. Not that it’s an exclusive privilege of interns, mind you! Anyone can find them in the “Muscle SpikerShield Bundle” kit.

With this bundle, you can do several very entertaining experiments such as seeing on your smartphone the action potentials that are produced when you move your muscles. You can also use the Muscle SpikerShield to control video games, robotics, and musical instruments.

It took a while for my board to pass customs, but it managed to arrive and we got to work right away. What I was most excited about was the arrival of new prototype from Backyard Brains – their very own customized Arduino board – codenamed NeuroDuino. (See above how handsome it is!)

Ben Antonellis, a guy who works for Backyard Brains, had created certain functions for a new interface called “NeuroBoard” that will make it easier for users to write working code for the Muscle SpikerShield / NeuroDuino. But the functions needed to be tested and verified by someone other than the principal developer. So, Tim asked me to do the testing and document the process.

Then came testing, testing, testing…

Testing Neuroduino
Natalia, Tim, Python and masks

So what we did at the beginning was try to understand the code that Ben created, where he explained to us a bit what each function should do. For this, we use the Arduino and C ++ programs. For example, we have commands to:

  • Start measurements
  • Find the greatest value of the channel measurements
  • Define the channel that we are going to use (if we select a different one from the one used, there will be no measurements)
  • Function to determine which button is pressed
  • Etc. (Still letting our imagination run wild!)

At first, we had a little trouble at understanding the commands and nomenclature, but we managed to test several of the pre-made functions. However, some did not work for us, so we asked Ben to help us figure out what we were doing wrong.

Ben helped us right away, tweaked the code a bit, and finally the three of us were able to test all the functions. Most of them worked well and some have yet to be modified. But we made a breakthrough, and now most of the code is tested and verified save for a relay function that’s still patiently waiting for its 15 minutes (or hours) of fame.

We are almost done with this phase of my internship, and for the rest of February, my final month, I will be looking into some custom Python analysis scripts.

Tim and I have been working remotely for the past two months, but we finally had a chance to work face-to-face this week (with social distancing and masks of course). The picture above shows how it went.

Stay tuned for my final blog post update at the end of February!


How to Get Reeled in By Neuroscience – a Mathematician’s Guide (Part I)

how to get reeled in by neuroscience

What lies at the intersection of math and medicine? Why many things, of course. Certainly more than could possibly fit into a blog post! But today, I am going to talk about the connection between brain function and numbers.

My name is Natalia Díaz and I am a student of Mathematical Engineering at the University of Santiago de Chile. Ever since I can remember, I have been tantalized by mathematics and medicine (especially brain function). The opportunity to mix both subjects finally arose when I entered college. That is how Neuroscience popped into my life!

To get my degree, I must complete my internship and my thesis. That’s how I started working with my mentors Dr. Patricio Rojas (University of Santiago) and Dr. Patricio Orio (University of Valparaíso). We are investigating, through numerical simulations, the effect of the electrical synapse topology between inhibitory neurons.

For this, we use a neural mathematical model of a mixed network of inhibitory and excitatory neurons of the cerebral cortex, and we study different types of topology (“all with all” or lattice style) of connection between inhibitory neurons characterizing the patterns obtained.

For example, the figure below shows a significant difference in network synchronization using different topologies. In the first yellowy-whitish graph, there is no gap junction (electrical synapse). The second shows a gap junction with a lattice topology, and in the last one we apply a gap junction with an all-to-all topology. To plot this, we use different values for the mean synaptic strength between excitatory neurons (mGsynE) and for the mean synaptic strength between inhibitory neurons (mGsynI). Lots of abbreviations, I know. But I promise they are fun!

neuroscience math medicine
The network synchronization using different topologies of connection between inhibitory neurons.

As I was researching internship opportunities, Dr. P. Rojas told me about Backyard Brains, a go-to company for those who want to tackle neuroscience through mathematics. As for my project, I will be working on our next generation interface products. Coding Neural Interfaces for beginners can be difficult to understand, so I’ll help make the interface by testing an Arduino library Backyard Brains has developed, seeing how easy it is to use, trying to “break” it, and improving the documentation on the library.

This way, someone using our Arduino -based products won’t have to start from scratch as they learn to control devices like robotics, computers, musical instruments, and video games with the signals of their bodies (EOG, EMG, EKG, and EEG). My project will last until the end of January, and depending on my time, I may roll up my sleeves and get into some Python data analysis programming, a long-standing data analysis dream for the Backyard Brains team.

In my spare time (before COVID), I used to travel to my mother’s house in Pichidegua (VI Region), where we’ve always got together as a family and had a good time, as you can see in the above photo. Yes, there are many of us – try to find me! But now due to the quarantine, I have only been in Santiago, which I also love because I can spend time with my boyfriend, Luis. He is very funny, and he’s also a mathematician.


Backyard Brains welcomes 2019 University of Santiago interns

Backyard Brains is now in its second year of interns from the University of Santiago de Chile (affectionately called Usach). Last year we had a project recording the ganglia of snails – and this we will continue our voyage in the world of invertebrates with an old favorite and a new favorite. Cockroaches and Clams.

The ElectrocardioCLAM

Hi, my name is Eduardo Isla, and I am in my final year as a student of biochemistry working at both USACH and UChile (Universidad de Chile). I am completing my undergraduate thesis right now as well as working for two months at the Backyard Brains Chile office. My thesis is in a quite different area (virology) working on epitranscriptomics of HIV-2. In my spare time I like to play MMORPG games as well as explore outdoor photography. 

A lot of high school students like Backyard Brains’ Neuropharmacology experiment, as you can indirectly study synaptic activity in crickets, but it is time for an upgrade. First, a little bit about neurotransmitters

Did you know that neurotransmitters were discovered working on frog hearts? Everything began in 1921, when an Austrian scientist named Otto Loewi discovered the first neurotransmitter. In his experiment, he used two frog hearts. Heart 1 was still connected to the vagus nerve, and Heart 1 was placed in a chamber that was filled with Ringers solution. This chamber was connected to a second chamber that contained Heart 2. So, fluid from chamber 1 could flow into chamber 2. Electrical stimulation of the vagus nerve (which was attached to Heart 1) caused Heart 1 to slow down its heart rate. Loewi observed that after a delay, Heart 2 also slowed down. From this experiment, Loewi hypothesized that electrical stimulation of the vagus nerve released a chemical into the fluid of chamber 1 that flowed into chamber 2. He called this chemical “Vagusstoff”. We now know this chemical as the neurotransmitter called acetylcholine. It is also interesting to know English scientist Henry Hallet Dale had previously isolated acetylcholine. So, they both shared the Nobel Prize in Physiology or Medicine in 1936.

For the Backyard Brains neuropharmacology upgrade I will use some Clams, yes Clams. We eat them, but they are animals too, and believe or not they have a heart. So, I’m trying to adapt Loewi’s experiments into much simpler animals, easier to access/buy and less traumatic to work on. These experiments consist of using the Backyard Brains Heart and Brain SpikerBox to make recordings of electrocardiograms on clam hearts and the effects of different compounds. For this, first of all I need to record an electrocardiogram of the heart of clams. Afterwards, I will then treat them with various compounds to attempt to alter the heart rate. I also need to ensure that the record that we actually obtain is EKG and not movement of the electrodes. In these first few days I am trying to optimize the preparation, opening the clam while keeping the cardiovascular system intact.

The Quantified RoboRoach

Hi, my name is Claudio Moreno, and I am also in my final year working at USach in the lab of Neuroscience. I am doing my thesis in ion channel physiology, studying TRPM8 channels. TRP channels are the body’s temperature transducers, and TRPM8 is responsible for the feeling of  coldness. In Chile we get cranky when the temperature gets below 40 degrees Fahrenheit (I know, nothing like Michigan), and we can thank our TRPM8 channels for that.

When not studying TRPM8 channels I enjoy going playing video games and guitar. I’ve being playing guitar for 13 years and it has been one of the best things I have done to get my mind distracted during moments of high stress. I also like to travel to different cities and countries. I have travelled to many cities here on Chile (my country), and it’s really beautiful, so if you have an opportunity to come here, trust me, you won’t regret it.

The RoboRoach is one of Backyard Brains’ original inventions where you can control cockroach locomotion by electrically stimulating the antenna, but, strangely, Backyard Brains has never systematically measured the adaptation rate. Until now. To do this experiment we are doing a bunch of RoboRoach surgeries, so we can have a high enough sample size to compare sensory adaptation rate.

Once a RoboRoach is recovered from the surgery, we can start to see if we can control our RoboRoach and measure turning responses with time! And for that we built a lego tower, which has a floating ball the cockroach walks on, along with an optical mouse to read the floating ball’s movements. When the antenna neurons are activated with electrical stimuli, they will send this electrical information (called spikes) to the cockroach brain, stimulating the neural-motor reactions. The cockroach will change direction, and we can measure this change.

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This contraption allows us to measure precisely the turning of the cockroach in response to stimulation of the antenna, so we can see how it adapts over time. Now it is time to collect the data and finally say with some degree of certainty the adaptation rates across cockroaches. Like all kinds of animals with a central neural system, you can expect that neurons can adapt to a stimulus (which Backyard Brains has anecdotally observed many times in the RoboRoach). Now it is time to quantify! I am starting to get skilled at the surgery, and below you can see my first successful antenna nerve recording!