From an Innocent Girl, to Undergraduate Actuarial Researcher

A year ago, I finished my high school degree in the United States, and was able to go back to China, the place I lived for 15 years. I visited my grandparents who raised me up and took care of my for my entire life in China, but I was shock by how much was changed to their health condition. People I care about the most is getting older and older, and suffering from different chronic deseases. I was sorrowful, and wanted to do something. That was the first time I truely realized my value of existing is to bring something valuable to the world, and to people.

I was lucky, because I got a chance that summer to explore this thing called research. I was selected to attend a 2 week research summer program: SIMS. That was my very first peak to the world of research. I was asked to rank a list of research projects as my favor to work with, when I saw one about investing cancer tumor cells, I put that on my top one without any doubt.

Two weeks passed really fast with an extremely packed schedule. I tasted my first fruit from the research experience: we truely got a data that can be a tiny contribution to approach cancer cure. I realized that research is such a fastinating thing that can really be a way for me to help people and the world. So I started to dig in more to learn about different research fields. I want to find the right one for me.

As an actuarial science major student, I didn’t realize there could be so many research topics to help with the world for this type of subjects as well until I met Mr. Duncan in actuarial association at UCSB. Besides being a professor at school, he is a successful actuary working in industry for over 30 years. But he is always passionate about researching and encouraging young researchers. I was totally amazed by how much papers and books he has published, and how respectful he is in actuarial field. At that moment, I realized I can do research and help people as well with math and statistics, these tools I am more comfortable with.

This summer, I am honored to work with Mr. Duncan on a research project about developing a predictive model on hospital readmission rate. While health care is often unaffordable for us normal people, especially those without health care insurance. With our model, we want to predict the hospital readmission rate for different types of patients, so that hospitals can provide enough care and attention ahead, so that hopefully to reduce the hospital readmission rate, and also, reduce the costs to go to hospital for patients. To make health care affordable is a big goal, but every little effort is worth trying and can approach to the goal closer and closer. I am sure that is true for all fields of research.

I have a great goal, that is to change the way people live, and help make our life and the world better. Innovation and research is the best way to real that goal. It might be a brand new area for those who never get in touch with research, but as you work hard, and find more opportunities, your research skills get better and better, and eventually, everyone can do their parts to help with the world.

EUREKA  Posted by 05 Sep 2019 / 0 comments

When your research results glow

E. coli glowing: Agar plate of E. coli, some with the red fluorescent protein gene

Staring at our plate, my lab partner and I couldn’t help but smile, tears and sweat dripping down our faces.

We had actually done it.

Our teacher had told us this would be a long, hard journey, and that some of us would not be successful. After this week-long quest, we obtained the red fluorescent treasure at the end. We were successful.

Everyone surrounded our plate and us, staring at it in awe as well.

My lab partner looked at me and said, “Our E. coli are literally glowing red! We did it!”

I first realized my passion for microbiology and research when performing a week-long experiment in my A.P. Biology course as a junior in high school. We conducted a bacterial transformation using recombinant DNA technology to insert our gene of interest– a red fluorescent protein gene– in a bacterium, Escherichia coli. As seen in the picture above, this gene allowed the bacteria to, well, glow red! It was a long process that, if not you did not follow the procedure exactly as stated and if you were not paying attention to detail, you would not get the end result.

This short but sweet experiment is a small scale example of what research is like. The process to get to an end result might be long and daunting, but once you get the result, it is like eating that cake after a week of being on a “diet.” I am painting the process as being unenjoyable, but on the contrary, it is full of exciting moments as well and each step encourages you to keep going. Even on setbacks, you learn from them and find new ways to tackle what you were working on.

As I mentioned earlier, my passion for research really started when doing this experiment. I had done other experiments, such as what factors affect the rate of photosynthesis in leaves and understanding the physiology of roly-poly bugs, but none really caught my attention as the bacterial transformation experiment. There are many branches of research that people can go into. You can be in a lab with a microscope, 60 feet underwater in the middle of the Pacific, or in the valley with hiking boots and a large bottle of water. I prefer to be with a microscope and pipette, looking at organisms that are much smaller than I am and understanding their importance and complexity.

Phytoplankton: Different species of phytoplankton collected at the Sea Center

Since there is such a diverse range of research topics, you may not know what you want to go into or what you enjoy most. It is important to try different research areas first. I knew I enjoyed microbiology, but that is still a broad category. I first combined my interest in the ocean with the smallest creatures that live in it: phytoplankton. I was in a laboratory that researched how climate-induced changes affect the physiological and community composition of phytoplankton.

Even though I enjoyed studying phytoplankton, I was drawn more towards the biomedical side of research. I downsized in the organisms I was studying to viruses, which are even smaller and less complex than phytoplankton but have huge impacts on individual people and communities at large.

In general, research allows you to explore your interests while also teaching you patience, new skills, and how to follow a procedure, because trust me, you’ll need to pay attention to all the details in order for your end result to glow as our E. coli did.

MARC  Posted by 03 Sep 2019 / 0 comments
chloe

How my Research Perceptions Changed

When I first envisioned research, I thought of a white coat scientist in a laboratory setting. I would never have guessed the EUREKA program would expose me to so many different fields of research. Research projects range from analyzing biochemical processes to coding computer programs and working with participants to examining complex mathematical functions. Although the term “research” can be associated to the cliche white coat lab setting and specific areas of study, the beauty of research is that it can be applied interdisciplinarily with the same goal of advancing knowledge and bettering society. Aside from that, I perceived research as a lone activity. With the experience I’ve gained so far in my lab, I’ve realized that I am constantly communicating with lab members about data analysis and various machinery. Research is a cohesive, team-effort and even includes communicating with people outside the lab such as official personnel and other faculty advisors. In fact, communication and connections are one of the most crucial factors leading to success in a research project.

On the other hand, I completely expected to be surrounded by intelligent and inspiring people such as my project’s faculty advisor, post doctoral, graduate students, and research assistants. Each colleague is an opportunity to learn something completely new and deepen my understanding of the project at hand. Additionally, I knew that research rewards hard work and continuous effort. Whether you are running a participant, analyzing data, or keeping up with the literature, you are responsible to have the initiative to do those things. By doing such tasks efficiently, you gain more information and skills directly tied into the betterment of your future. On top of that, expressing your interests and initiative to the lab members allows them to find ways to make your experience as beneficial as possible.

All the experiences I have gained from research were beyond what I imagined for myself and it’s a journey that every researcher takes. Research takes you down a road you never expect, and from there you decide what you can do with those skills. Ultimately, everyone’s research experience will be different and your perception of research will change over time in hopes to gain a better grasp of being a more valuable researcher.

EUREKA  Posted by 29 Aug 2019 / 0 comments

Female Alcohol Use Disorders are on the rise—and we don’t know how to treat them

Over the past ten years, alcohol use disorders (AUDs) have increased significantly—particularly among females. Although AUDs are predominantly male, the prognosis is much worse for females. They are much more susceptible to the negative consequences of drinking, such as liver disease and breast cancer.

This rapid increase brought forth an inconvenient truth.

Almost all of the studies that tested the safety of drug treatment for AUDs were conducted primarily on males. So, how are we supposed to treat these females with drugs that are not proven to be effective​ or​ safe? And how on earth do we not have that data?

Until 2016, almost all biomedical research was conducted mostly on male mice. Researchers use mice as models for humans, because their mammalian brain are similar to ours. A long time ago, however, scientists concluded that female mice were too hormonal to produce clean data. They have a 5 day cycle—like a mini human menstrual cycle—which results in hormonal variations that influence their reactions in various behavioral tests.

These hormonal fluctuations, however, are not limited to females.

Recent findings proved that when male mice are housed in groups with other males —which they are for almost all studies—their testosterone levels sky-rocket. These variable hormone levels also influence behavior, but have never been regarded as an issue or blockade to reliable data.

Have sexist biases have gotten in the way of objective science? Scientists completely disregarded females because they were hyper-hormonal and messy, without giving male hormones a second thought.

Recognizing this issue, the NIH issued a mandate in 2016, stating that they will only fund preclinical studies if they include female subjects.

This summer, I am working on a project that examines sex differences on the effect of adolescent binge-drinking. In order to develop an effective pharmacological treatment for female AUDs, we must first understand the neurobiology of their addiction.

There are years of research to catch up on, but we are headed in the right direction. Hopefully, we gain some insight into the nature of female AUDs, and begin the process of safely treating them.

EUREKA  Posted by 27 Aug 2019 / 0 comments

How to Teach Yourself Image Processing

1. Context

This summer I have been asked to write a program that will take the following picture of transistors…

…and measure lengths and angles of the gray shapes inside of each box. The scope of this writing is image processing so we’re not going to talk about what a transistor is or where the gray shapes come from. Just accept the fact that they exist and I’m trying to measure it. On to the image processing where the program I am using is MATLAB.

2. Binary Image

The entire process starts with edge detection: letting the computer decide where lines are. Googling edge detection tells you to start with converting the image into a binary image. Binary Images are the foundation of edge detection because there is a white pixel were a line is and a black pixel where there is not a line. To make a binary image simply type edge(image) into MATLAB and-

 

So it’s the first step and I have already come across an issue. The images I am working with are too noisy and produce real nasty looking pictures. So step 1 a) is to filter an image to reduce noise. There are multiple filters that can be applied and multiple methods for creating binary images and photos of these multiple iterations are below:

The best and most consistent thing that worked was the use if the ‘canny’ method for binary image creation and applying one filter.

So after all that, step one is completed on to step two.

3. Line detection

MATLAB has a built-in method for detecting lines called the Hough transform. It’s a popular method for line detection used in most computer vision programs today.

 

The graph is in terms of the length of the line (rho) and the angle it is at (theta). The brightest points are where the computer believes there is a line. Applying this to the current binary images I have yields…

 

An incomplete method for finding lines. Turns out the images I have are too pixelated to give clean lines to the program so MATLAB only finds the lines it is only 100% exist and anything else is left unnoticed. This led to a rabbit hole for finding other methods of line detection such as the Radon transform, and nothing worked. So eventually, I decided to tell the computer of multiple pixels are in a vertical or horizontal line then say it is a line.

Now I can find lots more lines. My next step was to make an outline of the transistor using the furthest outward line. As you may have guessed, there is a lot of room for error using this method.

This is an error I plan to fix later in the project because this does work on most samples I have. From this point I moved on to my next Step.

4. Meaningful Measurements

I currently have measurements in pixels, but pixels mean nothing to the Lab, so I decided to implement a method for recording the measurements in nm. There is a scale bar on every picture I receive so the easy approach is to use the scale bar to create a pixel to nm conversion.

Ahh yes, clearly defined lines in this scale will make this step trivial compared to everything I have done up to this poi-

Yeah this is an issue, being unable to consistently measure the scale bar leads to many issues as you may have guessed. So on to plan B. I noticed by this point that all photos gathered are in exactly two resolutions, and the magnification is consistent across each photo. Below are data points that show the best fit curve to describe the relationship between magnification and pixel to nm conversions.

MATLAB has a built-in word detector called the OCR which is a simple tool to use. I can find the phrase ‘mag’ and read the number underneath to find the magnification of the photo and use the trendlines from above to find the approximate conversion for pixels to nm. So now I have a consistent form of real -world measurements and my next step from here takes an exciting turn.

5. Object Detection

My next step is to use object detection to take a full photo of transistors and locate each one individually and perform all the steps described above without the need of the user to locate each one at a time. This is the meat and potatoes of computer vison you brag to everyone about and feel real cool about it. So how hard is it? Step 1: type imagelabeler into MATLAB. Step 2: draw boxes around what you want to find like so.

Step 3: repeat step 2 until mouse breaks. Step 4: run program and the result is…

Easy. All it takes is a premade algorithm and your sanity to do object detection. This is the progress I have made so far in my task but there is still more to do. So how do you learn image processing? The answer is to google everything and see what works for you. Hint: if your subject is really small then most things are not going to work on the first try.

Gorman  Posted by 22 Aug 2019 / 0 comments