Picking Outside the Box

Computer science, computer science and more computer science. This was how my first year as a computer engineering major here at UCSB felt like. It was the only subject I took every quarter that dealt with my major. Although the courses were fun and challenging, I was hoping to have a course that dealt with circuits. Therefore, when I was searching for a professor to do research with during the summer of 2016,Professor James Buckwalter’s page caught my eye. He was working with millimeter-wave integrated circuits that would help increase data rates. It might not sound to exciting, but to me, helping increase the speed at which devices receive and transmit data sounded awesome. Additionally, integrated circuits sounded complex and I love a challenge.

After emailing Dr. Buckwalter, and setting up a time to meet up, I had a question bothering me. How was I supposed to help with integrated circuits if I had no previous knowledge of circuits in general? Having the question in the back of my head, I met with Dr. Buckwalter introduced myself and spoke to him about my interest in his research. Dr. Buckwalter then asked me what year I was in and what courses I had taken. After answering his questions, he said what I was most afraid he would say. Politely, explained to me that I had no experience in circuits and therefore it would be hard for me to help them in their research. However, he proposed another project, in which I would scan the radio spectrum to search for underutilized frequencies. After giving me further explanation, I was worried I was not going to like the project, but at the same time I had come in asking to work on something I had no knowledge of. Unconsciously, my mouth opened and agreed to the offer. I was worried, I had little information of what to expect, what I was going to learn, and what exactly I would be doing.

Fast forward into today, I am glad to have accepted Dr. Buckwalter’s offer because radio frequencies and the radio spectrum are much cooler than I expected. Each frequency is unique and therefore travels in its own “lane” carrying information. Determining which lanes are open is my goal for this summer. By doing this, we can then use the lanes that are left unused and make the spectrum more efficient, allowing data rates to increase. As you can see, I am actually doing something similar to what I initially wanted to do, except I am doing it through the radio spectrum.

During the three weeks I have been in the lab, I have learned more information than I expected in areas I did not expect. For example, I learned the two different ways in which phones transmit and receive signals, the path the waves follow when they are received by an antenna, and how the frequencies are extracted from the waves entering the antenna. I find the extraction of frequencies to be the most interesting.

It turns out that there is an equation called the Fourier Series that tells us that any function of time can be estimated by a series of sine and cosine waves with different frequencies. For instance, the square wave below is really just a combination of infinite amount of sine waves.

 

Figure 1

Figure 1

Having this in mind, when scanning a specific range of the radio spectrum, many different waves with different frequencies are added together along with noise. Now noise are random numbers with a certain variance added or subtracted to the signal. Therefore, once the signal is plotted onto a graph, it looks like Figure 2 and it is practically impossible to tell what frequencies are present in the range scanned.

 Figure 2

Figure 2 

However, when the Fast Fourier Series (FFT), a fast way to calculate the Fourier Series, is implemented to the function, we can visually see what frequencies are in the function by seeing the big spikes in the FFT graph (Figure 3). In the case below only frequency 10(Hz) is present and therefore is showed by two spikes in at 10(Hz) and -10(Hz).

Figure 3

Figure 3

Anyhow, what I am trying to say is that when choosing a research project, be open about it. It doesn’t have to be on something you are an expert on. It doesn’t even have to be related to your major. In my case, it was within my major, but it was new to me. Now, it is not so new and I spend hours working on my project, sometimes skipping meals because I am lost in the world of radio frequencies. Hence, I encourage all to pick a project outside the box, you never know what you will learn about the topic and about yourself.

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The Layers of Medicine: My Summer at Stanford

“Can I get a 5:0 Monocryl and 6:0 Fast Absorbing Gut?” I thought after hearing Dr. Aasi repeat the remark over fifteen times a day through the span of my internship I would get tired of the phrase, but the request was precedent to surgery and watching Dr. Aasi perform surgery was number one on my list of preferred summer pastimes. During the short amount of time I was able to spend at Stanford Medicine shadowing Mohs practitioner and surgical oncologist Dr. Sumaira Aasi, I learned more about the nature of doctors and their teams than I did about the details of medicine. Of course I was intrigued by the effectiveness of Moh’s medicine in removing basal cell carcinomas and the many reasons skin grafts can die after being sutured to an open wound and the exact temperature of liquid nitrogen–all fascinating topics of conversation–but the paramount take away from my summer at Stanford was being able to observe the intricate workings of a hospital clinic.

Dr. Aasi and her team resemble a house of cards. It seems as if they can read each other’s minds, always knowing the whereabouts of every patient’s wandering family members and the next tool Dr. Aasi needs placed in her hand. The team flows, with every factor of the equation solved for. One nurse enters a room as soon as the first exits, the rooms are prepped just in time for the doctor to enter, and the slides are presented at perfect moments between surgeries. There is an unspoken understanding of the way things need to go. My first few days of the observership I was following Dr. Aasi around like a lost puppy, equally befuddled and awed at the clockwork that was their clinic.

The Outside: What Field of Medicine?

Dr. Aasi performs surgeries regarding lesions on the skin that can take the form of basal or superficial squamous cell carcinomas, cysts, lipomas, or keloids. Basal and squamous cell carcinomas are skin cancers that are contained in the outermost layer of the skin, the epidermis. The cells on the topmost layer of skin are called squamous cells, which are constantly shedding and being replaced by basal cells, located in a lower layer of the epidermis. Basal and sqaumous cell cancers are most commonly developed from sun exposure and poor sun protection. They are found in areas such as the face, back of the neck, arms, ears, or hands. The most  common type of skin cancer is a basal cell carcinoma, a slow growing cancer that is minimally invasive and rarely spreads throughout the body. A squamous cell carcinoma is less likely but has a higher likelihood of spreading to other parts of the body because it is found in deeper layers of the skin.

The two main surgical procedures to treat these carcinomas are Mohs surgery and excisions. The Mohs procedure is practiced when there is a skin cancer present on visible areas of the face. Mohs is beneficial because it preserves as much healthy skin as possible and keeps scarring to a minimum. This treatment involves subsequently removing layers of skin that contain malignant cancer cells and immediately sending them to the lab for analysis of leftover tumor. If cancer cells are identified under the microscope, the doctor goes back in to remove another layer of the skin, and the process is repeated until there are no leftover cancer cells. Similar to removing a rotten chunk of an apple, the removed portion is tested for residual impurities. The process is repeated until the patient’s slides are all cleared, Dr. Aasi averaging between one to three stages per patient.

An excision surgery is performed when the skin cancer is located in more conservative areas of the body such as the back, chest, or abdomen. The procedure removes a larger portion of the skin and cuts deeper than Mohs procedure. The doctor incises around a predictable margin for the tumor and immediately sutures the incision without waiting for lab results. Then, the sample is sent to the lab and the team notifies the patient of the results in a few days.

The Middle: What I Learned from Watching Surgery

The first surgery I watched was a Mohs procedure on the outer cartilage of the ear. After the nurses numb the area by administering shots of lidocaine with epinephrine, Dr. Aasi enters and incises around the tumored area. She gently holds and lifts the thin layer of skin using a pair of tweezers. Next she makes systematic cuts under the lifted layer of skin and runs them smoothly up the incised area until the entire sample is cut loose. Dr. Aasi also makes two grid-like cuts along adjacent sides of the incision to orient the sample in relation to the patient’s body. These grid marks help her understand what she is seeing under the microscope. The practice seems routine, almost too easy for Dr. Aasi’s experienced hands. Her steady, composed form makes the evidently complex operation seem simple.

The nurses take care of most residual duties such cautery and pressure dressings between stages, while Dr. Aasi is usually out the door and already halfway to the lab before I can even turn toward the exit. After each stage, the clinic sends the sample of skin to pathology where Dr. Aasi sketches the shape of the sample and applies a different color dye to each edge. These preliminary duties help her visualize a general map of the sample under the microscope. By adding the blue, black, and red dyes, Dr. Aasi distinguishes top from bottom and left from right in relation to the sketch, which is always drawn in regard to the patient’s left shoulder. The pathologists flatten and cut the sample of skin into several slides that are put through an automatic dye machine and then arranged for the doctor to read.

The first time I observed Dr. Aasi viewing specimens under the microscope I was baffled at the speed at which she zipped through the slides and made calls to clear the patient. While all the cells looked like identical blobs to me, she was able to differentiate between  the misshapen island cells of a tumor and the sweat glands, hair follicles, nerves, and normal skin cells the body produces. Over time Dr.Aasi taught me how to distinguish the cluttered, island like appearance of cancer cells from the rest of the body’s creations. Usually colored darker than the surrounding areas, they show up in clusters, resembling nests of irregularly shaped cells. If any tumor is seen under the slide, Dr. Aasi determines which area of the original sample the tumor is in based on the grid marks and dye she placed on the specimen. Characteristic of Mohs, in subsequent stages Dr. Aasi removes skin only from areas where tumor is still present, preserving as much healthy skin as possible.

The Inside: The Lessons That Changed How I View Medicine

While Dr. Aasi operates on patients she often strikes up conversations about random yet intriguing topics. We find ourselves talking about how classy the Obama family is one minute and the next Dr. Aasi will be reminiscing her college days and how she actually had to go to the library and read a book to do research. These spur of the moment exchanges characterize my most valuable glimpses into Dr. Aasi’s life. She discloses stories about her career in medicine, ranging from her experiences as an attending, the hardships of adjusting to new hospitals, and some of the scariest moments she’s had in an operating room. These stories inspire through character, they mean something because they make the hospital come to life, and it’s stories like this I hope I’m able to tell someday.

Through my time at Stanford I learned so much more than I thought I would. Not just about the nature of dermatologic surgery, which proves to be a job for a doctor, artist, and perfectionist all in one, but also about the unforeseeable speed at which life moves and the pure joy that comes from being able to help people. From hearing the stories of hundreds of patients and watching the doctor cure their illnesses, I got a firsthand glance into the miracles of medicine. After witnessing the pain and suffering associated with cancer, I was moved by the resilience of patients faced with circumstances beyond their control. I was stirred by the selflessness of doctors and the amazed by the rhythm of hospital clinics. I learned more from this experience than could ever be written in a textbook, urging me to learn by facing a constant rollercoaster of emotions. But most importantly I learned to never forget sunscreen.

 

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$ git commit -am “My research experience”

Your first reaction to the title was probably just like mine when I first dove into my summer research internship, EUREKA.

For this summer, I am working on Machine Learning and its uses in Computer Vision. More specifically we are trying to create a image recognition model that categorizes animals with a given picture. This involves heavy use of the Linux command line (aka bash) and Python; it also requires a time-consuming system setup so that everything runs smoothly.

At first, I was lost. I was trying to set up the system so I could use the Python library OpenCV. What do all these words and symbols mean?! I would scream internally while trying to read the endless stream of error lines. where in the wold is that bashrc file? Why do I need to install so many dependencies for this? Why are my training labels not being saved?! All these questions consequently led to never-ending browsing of StackOverflow posts, looking for guidance in the dark world of Linux. However, as days went by, I started seeing a shed of light in that dark place.

The best analogy that I can think of to describe this, is the process of solving a jigsaw puzzle. At first there’s so many pieces everywhere and it’s hard to pick a starting point. Many people (myself included) like to start on a strategic point, like the corner piece, because building everything around it is much easier. My “corner piece” were my CS classes – CS8, CS16 and CS24 – so I was somewhat familiar with Linux and basic bash commands. Soon enough, I started making connections. “So that’s how you add a PYTHONPATH!”. I had many “oooh” moments where things started to make sense,”No wonder why the changes on the bashrc weren’t taking effect, I wasn’t sourcing the file!”.

One after the other, and with the help of m awesome mentor, I slowly installed all of OpenCV’s dependencies, learning something new every minute.

“Phew! that was a nasty obstacle” I thought.  I was ready to get started on coding Python. I considered myself a good Python programmer, and I thought I was a bash ninja after setting up OpenCV. Turns out I was wrong in both cases.

My initial task was to implement a program that recognized digits in a picture. The purpose of this script is to recognize temperature values. As I Googled and browsed different people’s codes, I realized how much Python I didn’t know. “That doesn’t even look like Python code!” I thought while skimming through different pieces of code. Finally, I came across a well-documented StackOverflow post that I could understand. This was my “corner piece” to OCR and Machine Learning.

Fast forward all the bugs and problems I faced trying to make my code work.

Ta-da! My program worked. Not only did it have 100% accuracy on all different cameras but it also reads through 400 images in 20 seconds. It was 5 times faster and 30% more accurate compared to the code my PI used initially. With that I realized that I love programming. I love troubleshooting, looking at problems from different perspectives and “thinking outside of the box”.

The next task was to create/implement a program that recognized animals in a given picture. It sounds complicated, because it is and it’s something that top tech companies like Google and Microsoft are still trying to nail down. Luckily, there exists an amazing tool called Caffe that does exactly what I was looking for. It’s a convolutional neural network that takes in “training data” in order to learn to classify things. It even came with a default training dataset called Model Zoo, could you guess what it does? It recognizes animals in pictures!

Much like with OpenCV, Caffe also needed a time-consuming setup. Installing it was very similar to OpenCV but it felt easier, because I had learned where to look for answers and how to troubleshoot better.

It’s alive! I told myself when it was able to recognize an image of a deer as a gazelle. It worked, however it’s nowhere near perfect. It works well with nice photos, but not all the pictures that we have are good shots, especially because they are motion triggered, so often they are blurred, or pixelated because the lack of light to name a few issues. All these distortions make the program misinterpret animals, for example it recognized a bobcat that was far away as an armadillo and a bird as an impala (no idea how that happened). Currently I am in the process of narrowing down the choices that the model has to recognize. For example, we don’t have gazelles in California so if an animal is identified as a gazelle, it’s probably a deer.

I also started working on moving my scripts to remote servers so I can leave my program running as long as it takes for however many pictures there are – we currently have 900,00. However, the remote servers run CentOS, which is a different version of Linux, so I will spend the next few days on StackOverflow trying to install everything on a different system.

Let’s see where the command line takes me.

How Graciousness and Perseverance Will Land You That Next Internship

A personal anecdote touching upon themes of personal growth, academic excellence, and ingenuity. And how I scored an undergraduate research position in the best lab at UC Santa Barbara.

Personal Growth

“How do you land a position in a research lab? Magical beans? Fairy dust? Dashing good looks?” While I possess none of three unattainable goods listed above, I do accredit my current research position at top tier research institution UC Santa Barbara to a little lesson I learned in high school drama class: The Importance of Being Earnest.

Yes, yes. I will recall story that landed me my glamorous gig within the Zok Group, but first I would like to give context to my path less traveled by. I would have not seized the wonderful opportunities at UC Santa Barbara and previously if it wasn’t for my valuable mentors.

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Mentors share invaluable pieces of wisdom. Whether they are the faculty advisors, graduate students, or members of the graduating senior class, mentors will help you see what they couldn’t and push you to take advantage of the opportunities they didn’t. I have been very fortunate to have mentors that have taught me that while you cannot change the cards you were dealt, you can control how you play the hand. I encourage all students who are seeking research positions to find people with more experience than you whom you can connect with on a personal and professional level. These people, who often hang in the background, will open your eyes to new perspectives, write you stellar letters of recommendation, and share intimate experiences of overcoming adversities. Mentors are the manure of personal growth. While you have already planted the spores, they will help nurture the seedlings.
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Academic Excellence

I conducted research in my first lab through the Summer Institute of Mathematics and Science (SIMS). Although I participated in an equally rigorous engineering preparatory internship in high school called ESP, SIMS channeled the freshman college experience by creating opportunities and conditioning us to seize them so that we could set ourselves apart at the highest level academically.

We interns participated in eye-opening professional development situations where we were forced (for our own good) to connect with principle investigators of labs over casual dinner conversations. It was called Dinner  with Faculty, and it was brutal. It’s not everyday that you get to sit next to National Medal of Technology and Innovation recipient Arthur Gossard while chowing down on some non-vegetarian lasagna.

Contrary to popular belief, academic excellence is not limited to a high GPA but also encompasses your ability to communicate your ideas effectively and present yourself in an academically stimulating manner. Instead of asking questions like, “hey professor, what kind of research are you involved in?” Do your homework beforehand and instead say something like, “Hello professor, I understand that your group explores the functions of nanoparticles for targeted cancer therapy, and I am curious to know about the process behind designing experiments. What roles do graduate and undergraduate students play throughout the process?” Although you may not have a crystal clear understanding of what he or she is working on, asking informative questions will demonstrate your interest in their work and your motivation to learn more. Then, follow-up afterwards in order to inquire about possible lab positions.


Ingenuity

Mel, you still haven’t told us how you became part of a research group under a department that is world renowned for Materials Science! Well my curious and patient reader, I will now. See, success comes when arduous preparation meets luck, and boy was I lucky.

During the weeks following SIMS, my mind was already set on searching for opportunities that would allow me to experience the same personal and professional growth. I compiled a list of research experiences for undergraduates, commonly referred to as REUs. They all wanted the same thing,

“We would like to award internships to motivated individuals with strong academic background (GPA of 3.5 or higher recommend) and interest in conducting research in the fields of engineering, math, or hard science. Application requires transcripts, a resume, statement of purpose, and 1-2 letters of recommendation.”

My top choice on my short list was the Early Undergraduate Research Experience and Knowledge Acquisition internship (EUREKA!) And I got it. After going through an extensive application and interview process, I was awarded funding to pursue research in any lab that would be happy to accept me in.

Although my plan initially was to continue working in the biochemistry lab I had joined late winter quarter, a quick turn of events allowed me to change labs and begin working for a new graduate student mentor. It was a bright and sunny afternoon and UCSB’s 7th preliminary round of Grad Slams was in full swing. I had planned beforehand to attend the rounds with graduate students from the Materials Department. I did not plan on talking to any of them. However, after listening to a particular graduate student present on his current research: Designing New Materials for Jet Engines, I had an epiphany. I was so captivated that this kind of research was being done on campus that I sprung out of my seat after the competition ended and approached the graduate student.

“Hello, my name is Melissa Morales and I am a first year chemical engineering student … can I have a tour of your lab?”

I was so excited about this research that I whipped out my “talking to professionals” skill I developed during SIMS and eventually gained a new mentor out of it. After our initial meeting, I followed up with an e-mail and was graciously given a tour of the lab and time in the office where now current graduate student mentor shared photos of samples from an experiment he was working on. Laborious preparation truly met luck.


Now, let’s recap…

  1. I would have not thrived in environments like ESP, SIMS, or EUREKA if it were not for the wonderful mentors that guided me along the way.
  2. There is more to academic excellence than a high GPA. Having a strong network of knowledgeable individuals can help you complete unimaginable feats.
  3. When opportunities come a’ knocking, carpe diem. Be present and seize them.
  4. Success is when preparation meets luck.
  5. Be earnest in your pursuits and genuine with your endeavors. Work hard and connect with those around you because your network will help you get ahead, or refer you to someone that can. Be kind to others, show gratitude, and follow-up with those initial encounters. People will not care about what you have to say until you demonstrate how much you care about them. And lastly, contact the graduate students before the principle investigators.

Don’t Forget that it’s Summer!

After my first year as a physics major, my advisor and professor reminded my class to enjoy the summer— relax, travel, visit family and friends, do things that aren’t physics— this would be our last free summer before grad school.  I’m a physics major in the College of Creative Studies (CCS), which often makes people double-take.  They think: “Creative” sounds like an arts school, you’re a physics major?  While CCS has some phenomenal arts programs, the focus of the school is to promote creation.  Whether that creation be of new knowledge in science, an original piece of music, or a sculpture, the school aims to involve its students in the process of creation as soon as possible.  For physics majors like me, this meant an extra rigorous course load and researching with labs by the end of the second year.  Now that I’m entering my final year as an undergraduate and working my second summer in a lab, I’ve learned a few things.

Don’t forget that this is summer. This is a break in the school year designed to allow you freedom from homework, exams, papers, and daunting schedules (trust me, I know daunting, I’m hoping I’ll get my first opportunity to take less than 20 units this next fall).  Summer break is necessary for avoiding burn out and maintaining your sanity.  So, now you’ve chosen to complete a summer internship and have been awarded that opportunity. What about your break?  What about your sanity?

First, relish the fact that you have no homework, exams, or papers!  Then figure out your work schedule.  Personally, I aim to start working, whether it be in the office, in the lab, in the cleanroom, or at home, around 9:30-10 am.  Then I work

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Enjoying my morning skate to campus! (I may not look too happy because I’m trying to get a clear picture and not drop my phone!).

around whatever events are built into the internship and typically leave a little before 5 pm (most of my research group heads out then).  This doesn’t mean you can’t enjoy the freedom, weather, and relaxation of summer.  Take a walk down to the beach during the lunch break, or, in my case, when you start to go a little crazy after a few hours in the darkness of an optics lab.  Enjoy your morning commute, this is Santa Barbara!  Or in Reagan’s words: “…if not heaven itself, probably has the same zip code” in reference to Rancho del Cielo.

You learn very quickly that research is not fast, not instantaneous, but slow.  You will have time when you’re not sure what to do.  Because of this, you should often have things working in parallel, but as an intern, you’re typically just working on one project.  I use this time to knock out some of the internship side projects, presentations, and workshops.  Freeing myself up at 5 to go practice my trumpet, skateboard, surf, bike, socialize, play games, watch movies, whatever summer avails me.  During your time doing summer research, remember, it’s still summer.