The Kloepper Lab

of Bioacoustics and Animal Behavior at Saint Mary's College

How do you track a bat? Combining physics and computer science to investigate bat flight


By Alexandria Weesner

Like many people, I went through middle school and high school with an intense dislike for math. I didn’t like doing it, I found it boring and difficult, and I wasn’t very good at it. So it’s a little strange that I ended up studying a field that wouldn’t even exist without it.

My revelation happened during my senior year of high school. At the time I was taking Physics 2, because of my long-time interest in astronomy, and Calculus. When we learned in Calculus what a derivative is and how to take them I had a “Eureka!” moment. This derivative thing was exactly what we had been doing in my Physics class to find the velocities of objects, the only difference being that we hadn’t given a name to the process we were doing. Teachers had been saying my whole life that “you’ll have to use math in the real world!” and I didn’t see it until that moment. Calculus isn’t just used in the real world, it is actually the tool we use to describe how the whole Universe works! It sounds silly, but I was so excited. I went home talking to my parents about it, and I knew from then on that Physics was what I wanted to study. 

I graduated from Edwardsburg High School feeling very excited to go to college and start studying Physics. My plan had always been to move away from home and go to a big university. However, life always has a way of deterring our plans. When I realized what a financial burden going to a big university was going to be I ended up applying to and attending Indiana University South Bend, a decision that I am now very happy with. The department is small enough that the professors are able to dedicate time to help their students. I also made a lot of good friends that I wouldn’t have met otherwise. I am now a senior at IUSB; if all goes well I will have my Physics degree in hand this May (2020). 

If I had to give one piece of advice to any undergraduate student my tip would be: ask for help, always. Your professors and advisors are there to help you. An important part of studying physics (at least for those who are planning on going to grad school) is doing research, and it will help you out immensely if you can do some research as an undergrad. Every one of my research experiences happened because I asked my advisor, other professors, and even complete strangers for help. As an undergraduate I have worked at the University of Notre Dame doing research in a galactic archeology, Louisiana State University, where I did an REU with a LIGO-affiliated group that studies quantum optics, and at my own school, IUSB, where I have done work on the PICO dark matter experiment and on another project designing shark bycatch reduction devices. I now work at Saint Mary’s College with the Kloepper Lab Group, where I will continue doing research for the next two years. 

Screen Shot 2020-03-24 at 9.45.47 AM

Image caption: A photograph of me at the end of the summer of 2018 presenting my poster on the work I completed during the REU at Louisiana State University.

The project I will be working on in the Kloepper Laboratory is particularly interesting and special due to its interdisciplinary nature. Ultimately, it is a Biology project, but those working in our group come from a variety of backgrounds, including Biology, Physics, and Electrical Engineering. In the past I have only worked with other physicists; I learned a lot from those experiences, but I feel I have learned even more in the few short months I have spent here at Saint Mary’s about collaboration, good communication skills, the benefits of a group composed of a variety of backgrounds, and even Biology, since it is a field I have not studied before. 

Our main goal is to study the flight patterns of bats, which we are doing by developing a computer program to track and count the bats as they fly. We also want this currently-unnamed program to be able to do other things that will help biologists, such as sample colors measure lengths and angles of organisms, in addition to the tracking feature. It is important to us that this program be available to use by anyone who can benefit from it, like smaller universities that don’t have the funding for professional programs, high schools, and amateurs, so we plan to make this program free to use. 

Right now I am working on improving the tracking algorithm. It can already analyze the number of bats present in each frame of a video but it isn’t accurate when the bats’ flight paths intersect. If more than one bat overlaps in the field of view then the program will either count them as one bat or it won’t count them at all, which depends on the user’s settings. I am improving this feature by creating a program that takes images of the two bats from before and after the intersection, predicts what they will look like when they intersect by merging these two images into one, and finds the correct combination that most closely matches up to the reality. An example of this is shown below.

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Image caption: A sneak peek at the program I have written that predicts what two bats will look like when they intersect in the field of view of the camera. The image on the left is a real photograph of what the bats actually look like, and the image on the right is the prediction made by combining images of the two individual bats into one.

I will be sure to post more details and information on this process in the future! If this process proves to be unsuccessful or too difficult for larger numbers of bats then we will move on to training a neural network to detect how many bats are overlapping. At this point in time it isn’t clear which technique we will end up going with. Regardless of the direction we end up usingI am excited to see the results. 

I find it interesting how I started off with such a strong dislike for Math and now it is something that I use every day; the predicted image of the two bats shown above was something I created using my knowledge of Math, some programming, and a computer. Being able to do something like this wasn’t what I saw myself doing when I was a lot younger, but now I am just excited to see what else I can accomplish.

Second Chances

By Morgan Kinniry

If we have crossed paths in any capacity over the past calendar year, then you probably know that last summer I was an undergraduate research assistant for Dr. Kloepper’s summer field trip to the bat caves in New Mexico—and LOVED every minute of it. When I got back from the field, I got such a rush out of sharing experiences I had in the field, or the current work the bat data was bringing me to at the time whether that was a conference, a Bat Lab outing, or senior comprehensive work. I was a woman charmed by the bats.

As the school year went on, my senior comprehensive work drew to a close, and it seemed as if the field trip to New Mexico and time in the BatLab would begin to become a memory. I had my sights set on grad school and graduation. However, life had other plans. Soon enough, I found myself with a shiny new bachelor’s degree and a year of free time! While I tried to make sense of the whirlwind of transitions beginning in my own life, the opportunity arose from Dr. Kloepper for me to join the Bat Belles to their Summer 2018 field trip. Without any hesitation, I knew that was where I was supposed to be and signed on for a second summer in New Mexico. I was given a gift few can claim—a second chance.

The entire experience of having a second chance to experience a place that holds such meaning and had impact on me a year ago has been so surreal. I am able to witness things that I once thought I would never see again. A year ago, all of the New Mexican experiences I had were a ‘once in a lifetime’ opportunity. Yet somehow, I found myself getting to experience another cross country road trip, another stay at the ranch, another bat emergence, another buffalo encounter, another green chili cheeseburger, another mass at Our Lady of Perpetual Hope, another desert sunset, and another starry night sky. Life has a funny yet remarkable way of working out this way and sometimes it’s as if the next right move falls right into your lap. To add to this joy, I also get to experience the amazement and wonder in the eyes of Kate and Lily who are experiencing this for the first time.

Amid all of the pressures of young adult life that come with being a new college graduate, time in New Mexico away from the “real world” doing something I truly love and enjoy has given me the clarity of mind to recognize an important perspective: life should be spent pursuing the experiences that bring joy. This has been particularly meaningful to me at a time where the pressure is on to chase the “right” post-grad moves that our culture of comparison seems to direct me towards. So many things seem to get in the way of this simple truth.

Luckily, each night as I look up at the bats taking flight, I am remembered in a spectacular way to embrace the moment, enjoy where I am, and forge fearlessly ahead to wherever life takes me next.

To The Bat Cave!

by Lily Zusi

Wow! We arrived in Truth or Consequences only three days ago, and I hardly know where to begin. We left South Bend at 4:00am on the 30th, and after a full day of driving we spent the night in Amarillo, Texas. We enjoyed a pretty good night’s sleep and woke up to a Texas-shaped breakfast (you know, in case we forgot where we were).

A wholesome Texas-shaped breakfast

We had a lot of fun music downloaded for the trip in anticipation of the 23-hour drive, but Dr. Kloepper’s newfound podcast proved to be the most entertaining thing we listened to. The podcast followed a team of people who completed a year-long simulation of what life on Mars would be like for a colony of humans right now. The simulation took place on an island in Hawaii, and sounded surprisingly similar to what was in store for us- conducting research while physically isolated from the rest of the world, experiencing a lag in outside communication, living in a reduced space with several people you have never lived with before, and all in an exciting and alien environment! Their description of going outside the living space and into the Martian atmosphere in the Mars simulation sounded a lot like what Dr. K’s description of entering the bat caves would be like. The podcast was entertaining and well done, and made me even more excited than I already was to start my summer research experience.

Crossing the Rio Grande

We got to T or C about midday the next day and after shopping and settling into our bunkhouse, we got into our field clothes and snake guards and headed to the cave to observe the bat emergence. We ended up waiting for about 3-4 hours outside the caves before emergence began, but it was well worth it! A few thousand bats suddenly emerged from the depths of the cave in their column shape and flew right over our heads as they went to start foraging for the night. As if that wasn’t cool enough, nine Swainson’s Hawks showed up soon after emergence began, and began swooping at the bats just a few feet above us. I felt like I was in some National Geographic documentary- it almost didn’t register.  It was magical and wonderful and I still can’t believe I get to watch it happen EVERY NIGHT!

The next day we spent assembling our bird blinds, which we use to keep ourselves more hidden from the hawks to encourage them to stay close so we have a better view of their behavior. I personally learned a lot that day- what grommets are and how to make and use them, and that a PVC cutter is potentially the coolest tool ever. We turned on some middle-school throwback tunes and took turns grommet-ing to the beat.

Yesterday we actually got to go inside the caves with Dr. Kloepper, which was yet another amazing experience. We headed out early in the day to beat the heat (it was already 85 degrees at 8am), got fully suited up in our respirators and full-body Tyvek suits, [picture?] and took turns being led by Dr. K through both caves that the bats live in. It was such a unique and wonderful experience to walk around in the bat guano (I must have chosen the right major) and to be able to see where the bats roost in their clusters – they really pile up on top of one another, it just looks like a conglomerate blob until one pops out and flies around! They flew so closely around me that I kept thinking they were going to bump into me, but they always managed to avoid me at the last second. It was very, very cool.

Our first two nights (yesterday and Friday) recording the hawks and bats during emergence were hectic and challenging, yet super fun. Our fancy cameras have really come through for us, and we’ve taken some amazing footage of the hawks and bats already. Both emergences took place against a breathtaking New Mexico sunset!

Sneak peek of the footage we’ve captured
It’s easy to see why they call it the Land of Enchantment

Although we are only a few days in, we’ve been having a lot of fun and already have many traditions- whether it’s putting up our own “__ Like A Champion” signs each day, bringing a small ceramic bird stolen from Kate’s aunt’s kitchen table and affectionately termed “The Jester of Birmingham” as our good luck charm to emergence

The Jester of Birmingham

, or lining up and fist-bumping our hawk mascot, Robert Hawkins, before heading to the field. Other things that I predict will become tradition are making household items into workout equipment, whether it be turning water gallons into weights or bathroom mats into yoga mats, and Kate and I discovering even more random interests we have in common (Marvel, musicals, ballet are just a few of the things we’ve found we have in common).  I have already absolutely fallen in love with New Mexico- the ranch we are on has a gorgeous landscape and beautiful wildlife. In addition to Brazilian free-tailed bats and Swainson’s Hawks, we’ve seen all sorts of things I wouldn’t see in South Bend -jackrabbits, nighthawks, antelope, oryxes, quails, all kinds of lizards, herds of bison, and even a female bison with a newborn (like-just-born-five-minutes-ago) calf. I haven’t seen any cougars or heard any rattlesnakes yet, but then again, I’ve only been here for three days! I can’t believe how much has happened and how much I’ve learned in just these last few days alone, and I can’t even imagine how challenging, rewarding, and amazing the next few weeks will be.


Belle Bats forever!

Another field season is underway!

By Dr. Kloepper

Another field season is underway! We left the road at 4am on May 30 from Saint Mary’s with a rental Suburban full of field gear and positive attitudes. This year we had a full car–Kate and Lilly (rising seniors) and Morgan (SMC Belle Bats alumna). We prepped for a long day on the road with enough snacks for 20 people and plenty of upbeat playlists. We all shared driving duties, rotating every 2 hours, which allowed people in the back to get some much-needed naps. We also listened to the entire Habitat podcast, about people living in a small house for a year isolated from everyone else, unable to leave except in a space suit. Habitat is a real research project funded by NASA to help understand the psychology of humans living on Mars. We joked at the remarkable similarities between living on “Mars” and living in our small bunkhouse for a month, isolated from all signs of civilization.

The drive went by remarkably fast. We stopped in Amarillo, Texas, for an overnight in a hotel, then pushed on through to New Mexico the following day. We enjoyed the sites on the road, like this massive wind turbine blade:


And made sure to stop to get a picture of the girls (Lily, Morgan and Kate) when we hit the New Mexico border:


Just outside of Albuquerque, we stopped to say hi to Belle, who was busy being trained for her upcoming field work next week:


We stopped in Truth or Consequences to stock up on groceries, then continued on to the ranch. We had plenty of time to unpack and get the house squared away before we went to see the emergence. It was so rewarding for me to see the look on everyone’s faces when they watched the bats—Kate and Lily seeing emergence for the first time, and Morgan experiencing it for year two. I think I spent more time watching them than watching the bats!



After the first night of observing, it was time to get to work! The next day we built our bird blinds, which allows us to video the hawks that feed on the bats. By being hidden away, we reduce the chance of our behavior influencing the animals. The girls learned how to grommet and we had fun pounding away the rest of the afternoon. We assembled our blinds right outside of the cave, and we have now had two nights of successful data collection. We are all doing focal follows of hawks—Kate and Lily with video cameras, and Morgan and me with binoculars. We have started to get into the routine of data downloading, archiving, and analysis…we are all settled in and ready for a month of intense fieldwork and data analysis!

Dusty, Sweaty, Happy

By Kate McGowan

The Belle Bats successfully completed our second full day in the field! During our first two days, we prepped and sorted equipment, created game plans for data collection this summer, built two pretty awesome bird blinds, and spent two eventful days in the field! We are sweaty, dusty, and having a great time. Here are some things we have learned in our first couple days:

  • First, there’s no way to describe the magic of seeing your first bat emergence. Videos and words cannot do justice to how awe-inspiring it is to watch thousands of bats fly directly over your head from the cave, especially once the Swainson’s Hawks begin swooping in and out of the emerging swarms against the backdrop of a sunset sky. Truly nature at its finest.
New Mexico Sunset
  • Self-teaching ourselves to manually focus and zoom on fast moving objects was challenging, but well worth the videos we are able to capture of hawk attacks on the emerging bats.
Bird mascot “The Jester” taking field notes
  • Learning to grommet was much more exciting than expected, and we discovered one way to judge the quality of a song is by how successfully you can grommet to its down beat.
  • We do a lot more collecting and throwing rocks than anticipated: grabbing rocks for throwing at other rocks to check for rattlesnakes, moving sharp rocks out of the dust rock to avoid tire damage, collecting rocks to weigh down our bird blind, marking locations of equipment with piles of rocks, stabilizing the SM3 Acoustic microphone tripods with large rocks, etc. Lots of rocks in desert field work.
  • Whether you wanted to or not, you will develop new appreciation for Sweet Home Alabama (car ride theme song).
  • Jackrabbits appear to place little value upon their lives. This is demonstrated by how frequently they choose to run towards the car headlights rather than away from them.
  • Being inside bat cave is the closest thing to scuba diving on land that I have ever experienced. Like diving, you move through an alien land with limited visibility, focusing on keeping your breathing controlled through your respirator, looking through your mask in awe at the foreign scene around you. It’s truly a unique and bizarre environment. Some differences from diving, however, include that the cave is exceptionally hot and rather than a wet suit, we are clad in a Tyvek suit (feels like someone wrapped cling wrap around you in 100-degree heat). Also, the dunes in the cave are not composed of sand, but mounds and mounds of soft, dried guano. I was also surprised to observe that the bats are not spread throughout the cave, but cluster together in a large clump of thousands on the cave ceiling. I feel so fortunate to have such an incredible experience.
  • No matter how fast they may be trying to flee from you, all the quails I’ve seen still run in a single file line.
  • Verizon may actually be “America’s Most Reliable Network,” as only those with Verizon have signal on the ranch (I have AT&T). While I may occasionally miss sending a text or making a call to friends or family, having no service can be refreshing. We’ve spent time drinking coffee while looking at the mountains, getting in extra camera practice, reading, doing group yoga, having meals together, trying to figure out answers to weird questions ourselves rather than googling them, etc. Or if you are Kate and Lily, you may spend a great deal of your time having repeated conversations surrounding the plot of Infinity War or various Marvel theories (no spoilers).
View from backyard
Camera Practice with Lily
  • Lastly, bats will make you wait, but bats will wait for no one.

Looking forward to many more lessons and life skills! Today, we are headed into Truth or Consequences, where I’m really looking forward to trying the green chile cheeseburger that Morgan and Dr. K keep talking about. Bats forever.

One More Day!

By Kate McGowan

Almost two years ago, while sitting in an English classroom, my attention was drawn to a fellow student when I overheard her say “bat cave road trip.” I began actively eavesdropping on her conversation and learned that she had spent her summer on an extended road trip traveling from bat cave to bat cave and conducting research with another student, a biology professor, and the professor’s dog, whom had used as a pillow while they had been hiding in a bathroom at 3:30am on a stormy night while camping. My immediate thoughts: Where and how do I sign up?

Come two years later, and we are only a day away from this summer’s bat adventure! In 24 hours time, Dr. Kloepper, Lily, Morgan, and myself will be boarding the SMC Belle Batmobile for a 23-hour drive to Truth or Consequences, New Mexico. We are eager and excited to get on the road! Lily and I have been working on a playlist for the long drive, although this playlist so far only contains one song (called “We Are All Bat People”).

Amongst other various projects, my primary focus this summer is to study the predator-prey relations between hawks and bats. This project is split into two parts, with Lily focusing on characterizing hawk attacks while I investigate the acoustic and flight dynamic response of bats to predation threats. One of the most difficult and exciting aspects of this project is the lack of previous research on bat response to predation: nobody has studied it yet! This also involves using the help of a trained hawk named Belle, who is equipped with video and acoustic recording devices to collect data as she flies through emerging bat swarms. Additionally, I will be continuing a project that focuses on how bats adjust their echolocation calls as they move from open spaces to the cave edge when reentering the cave after foraging.

Our prep for the summer has consisted of memorizing various raptor species native to New Mexico, learning how to use SM3 wildlife acoustic microphones (and removing the centipedes they had accumulated from being in the Saint Mary’s nature area), sorting through field supplies with Dr. Kloepper, and self-teaching ourselves how to use the video features on our “fancy” Lumix cameras. This includes learning how to use manual zoom and focus when filming moving targets in order to practice for filming raptor attacks on bats in the field site. To practice, we’ve gone on multiple field trips – Notre Dame, St. Pat’s Park, Potato Creek, etc – to film any moving wildlife we can find. We now have portfolios of geese, swans, turtles, the golden dome, snakes, ducks, and more geese. While this was initially a challenge, we are loving the new cameras! Future nature photographers?

I am honored and excited to be a member of this team, and I cannot wait for our adventure to begin! To the bat cave!

Coming into Focus

By Lillias Zusi

I can’t believe it’s almost time to start our New Mexico journey! We have been working to finalize our research projects all semester, and have been packing and preparing for the summer for the last two weeks. The time has absolutely flown by! It seems like just yesterday I was frantically trying to choose a senior comprehensive topic while finishing off my semester in Australia, and now here we are!

A big part of our prep over the last few weeks has been to list and practice identifying all the different kites, hawks, and eagles that we could potentially encounter during our research… and there are a LOT! We will have to be able to identify them in the field, usually from a distance so we’ve been practicing distinguishing different species from each other. Thank God for Quizlet! Another big part of our preparation includes spending a lot of quality time with our new fancy cameras. We’ll be depending on them for most of our data collection, so it’s important that we figure out how to follow fast-moving birds. Kate and I been heading to nature-heavy areas here in town like St. Pat’s Park and Potato Creek, and have filmed everything that moves – ducklings, families of geese, songbirds, fish-catching ospreys, swimming snakes, frogs, turtles, … and occasionally each other.

A wild Kate appeared!

The hardest part of figuring out our fancy cameras has probably been getting skilled at using the manual focus while zooming in and out. Hopefully we’ll master that before we start our recordings of the hawks and bats…

When we aren’t pretending to be freelance nature documentary photographers, we have been learning about all the different recording equipment that we will be using in the field as we pack it up and label it. We’ve been doing everything from getting crash courses in Electrical Engineering from Dr. Stevenson to learning how to efficiently pack scientific recording equipment from Dr. K.

Packing up all the electronic equipment requires a LOT of labeling!
Look out world, we’ve got sharpies and we’re ready to label.


In addition to all this, the past two weeks have also been full of bat-themed puns, strange insect-themed rock music, impromptu nature walks, bonding time with Dr K’s adorable dogs Kaipo and Kona, lots of laughter, and LOTS of freelance photography material.

We leave in a week from today! I can’t believe how much I’ve learned in these two weeks alone, and I can’t wait to get into the field. I’m so grateful to Saint Mary’s Biology Department and Dr. Kloepper for this incredible opportunity!

Until next time!



UntitledWritten by Makenzie Duncan

Two days ago, I returned from Auburn, Alabama where I conducted microbiological research involving the bacterial communities hidden in bat poop at Auburn University. Yes. You read that right.

For the last two-ish weeks, I accompanied Dr. Kloepper’s transition from the field to the lab with our microbiology Yoda John McInroy, and it was filled with what seemed like endless amounts of agar plates, Southern barbecue, early bedtimes, and excitement.

When we had our first day in the lab on June 13th, Dr. Kloepper and I both didn’t know what exactly to expect. Though I have some microbiology knowledge (many thanks, Dr. Khadka!), I, too, am an organismal biologist through and through. I never would have guessed that in just a week and half’s time, I would grow to actually enjoy running PCR gels, staring at collections of As, Gs, Cs, and Ts, culturing seemingly innocent colonies of bacteria to find that they could rip my blood cells for food, and more thrills of being a microbiology novice.

When we first entered the lab, we quickly scrunched our noses to the potent smell of cultured plates and gawked at the first round of bacteria we would study. This would be the first of several lines of cultures that we scrutinized for the next week and a half, praying that we could get something freaky to grow. By the end of our time in the Kloepper laboratory, we had successfully cultured and isolated 99 samples (and we have more in the works!), some of which we have already identified. Who would have thought that two organismal biologists and one microbiological sage could have carried out such a feat? We were also able to take our samples back to Saint Mary’s, where they will hibernate in the -80°C freezer so that another Belle can eventually continue this research. Our poop treated us well and left us with many questions that we hope we can address and answer.

All microbiology aside, I discovered many other new things during my time in the South. I learned that humidity can truly make you feel like it’s raining outside even when it’s not. I learned how to de-seed a tomato, make savory oatmeal, run uphill correctly, watch Naked and Afraid without thinking it’s the strangest thing I’ve ever seen, and wake up before the sun rises without being a total grumpy pants. I had the chance to meet Dr. Kloepper’s awesome family and be a part of a remarkable collaboration with a major university—and I don’t even have a degree yet!

Now that we have made the 12 hour drive back (and listened to another fabulous crime podcast), my current homework is to collect information regarding the pathogenicity of bacteria found in a bulk collection of guano for a manuscript that we are completing with Molli, another member of the Auburn lab family. Pray for me—this is one of the longest Excel sheets I’ve ever seen! After that’s done, I can begin formatting my senior composition, and that makes me both super excited and terrified at the same time, but mostly excited. J

Thank you for all of those who sent kind thoughts our way throughout the trip. It was a life-changing week and a half filled with both the typical and atypical ups and downs of research and I am so honored to have had the privilege of being an Auburn Tiger for a short time. Thank you to Dr. Kloepper for allowing me to accompany her on this terrific journey into the lab and for letting me load most of the PCR gels :), to John for guiding both of us to not contaminate our data, and to Saint Mary’s for allowing research to continue to grow at our institution.

War Eagle, Belle Yeah! Makenzie


18 Things Learned During a Month in the Field

By Morgan Kinniry

The Belle Bat team just arrived home from a month of working at our field site in New Mexico. This month was one of the most incredible and fun experiences that I have ever had the pleasure of taking part in. During my time at the field site, I kept a running list of things that I learned to share with those who couldn’t be there. Please enjoy the list below of some of the things I learned over the last month:

  • Rattlesnakes sound like sprinklers.
  • Desert sunsets/sunrises are the best
  • The scent of bat guano can become kind of endearing with time
  • The Milky Way looks like a sparkly cloud
  • Harris’ Hawks make great biological drones
  • Mechanical drones sound like a swarm of bees
  • Fast flying bats sound like zippers
  • Bat emergence waits for NO ONE
  • Baby bats are pink
  • Baby buffalo are red
  • Asking locals (during mass) is the best way to find a good lunch spot
  • Oryx have impressive antlers
  • Bats are not afraid of drones
  • Trader Joe’s bags are GREAT for carrying anything/everything
  • Desert dust is very apt at finding its way into everything
  • It’s possible to live for a month without internet or cell service
  • Running a 5k is possible
  • The rumors are true: dry heat is truly more tolerable than humidity

I am so grateful to Dr. Kloepper and the Biology Department at Saint Mary’s College for allowing me to take part in this experience. Now I just need to analyze data and write my senior comprehensive!


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