MicroRNA Regulation of Plant Innate Immunity"
My research in the Baker lab works to further understand the molecular-genetic mechanisms of plant innate immunity. Specifically, our lab looks to analyze plant microRNAs and small interfering RNAs which allow plants to regulate development, genome function, and immune response. This semester, I have been utilizing bioinformatic procedures to download and format RNA sequences from other genomic databases in NCBI and analyze them using software like NCBI’s BLAST and SnapGene. Through this analysis, we were able to observe how conserved certain genes were across different plant species. This summer, I look forward to continuing to help develop our lab’s SOMART databases and hopefully get experience in an in-person lab environment....Read More about Matthew Huh
Integrated Activation Maximization"
Despite their popularity as predictive models, interpreting deep neural networks is still an open problem in machine learning. While local attribution techniques such as Integrated Gradients provide an importance map for individual input vectors, these techniques are unable to efficiently provide a global importance score over the entire input space. We introduce Integrated Activation Maximization (IAM), an iterative algorithm to jointly extract the activation maximizing pattern and a global attribution map for any node in a neural network faster than competing global attribution methods. IAM conducts a regularized gradient ascent to find the activation maximizing pattern for each node, while iteratively guiding the gradient ascent with on-the-fly feature importance estimates. IAM thus produces (1) a localized and focused optimal input pattern which emphasizes the features the model is most sensitive to, and (2) an attribution map that quantifies the importance of patterns in the optimal input....Read More about Doseok Austin Jang
Deep Learning for Improved Clinical Cancer Care"
The prostate-specific antigen test (PSA) is a blood test used primarily to screen for prostate cancer. However, single PSA values can be hard to interpret due to noise and fluctuating baselines. This summer, I will be continuing my work at The Hong Lab at UCSF where we are applying deep learning techniques to EHR data in order to better understand PSA growth in potential prostate cancer patients. By taking into account both a patient’s clinical data over time as well as certain demographic features, we hope to build a tool that can accurately predict a patient’s PSA value three months into the future. Further, we hope this research will shed light onto how PSA baselines may vary according to these demographic features so that clinicians can be better informed when making decisions regarding potential cancer cases. To do so, we will be developing a pipeline to best interpret the sparse […]...Read More about Morgan Lafferty
UC Mentoring Landscape "
Throughout my time at UC Berkeley, I’ve learned of the difficulties of navigating different spaces academically, professionally, and socially first hand and the importance of having supportive peers and mentors. This summer I will be continuing my research on conducting a landscape analysis of mentorship opportunities here at the University of California, Berkeley. In particular, this landscape analysis seeks to see if being involved in a mentorship program will lead to long-term career success, especially for Underrepresented Minority students and students from a non STEM background....Read More about Jason Lam
Hong Kong Arts and Visual Culture"
In this summer project, I will continue to assist Prof. Wong in building a database collection that consists of a timeline of Hong Kong art history, various bibliographies, as well as artist lists. I will also continue working on an ongoing digital resource page that is made up of online archives, photography, and local exhibition catalogues. We are currently expanding the project to include the diasporic HK artist community in order to explore the relationships between arts/culture, politics, and the HK identity. Due to HK’s political turmoil and an increasing suppression in artistic freedom, this project is particularly important in preserving existing works that constitute the unique culture on the other side of the world....Read More about Chung Lam Law
Polyubiquitination of Tau in Alzheimer's Disease"
A key indicator of Alzheimer’s Disease (AD) is the progressive accumulation of tau in the brain; tau is a toxic protein that ultimately leads to neurofibrillary tangles, but the specific mechanisms of toxicity are still unclear. Our collaborator Judith Steen, a professor from Harvard University, conducted studies using proteomics in cells and detected that in AD, tau gets polyubiquitinated, but the same effect is not observed in other tauopathies. To validate this observation, we have used Tissue Microarrays (TMAs) of cases at progressive stages of AD, which have undergone multiplex immunostaining for tau, neurons, glia and 2 other polyubiquitination markers. Over the next few weeks, I will scan each of the TMAs, count cells in the different channels (NeuN, GFAP, CP13, etc.), and run a co-localization macro to validate the findings from Professor Steen and potentially point to possible mechanisms of toxicity....Read More about Yoobin Lee
Identification of Inconsistent Families in SCOPe database"
Proteins often fold into compact structural units known as domains, which are the basic units of protein function and evolution. Delineating domain boundaries is a pre-requisite for further analyses of protein structures, but the accuracy of computer programs is still not satisfactory. With the support from my mentor, I have surveyed the current version of SCOPe (Structural Classification of Proteins – extended) database in the last two semesters: I have found and labeled/corrected protein families in which different structures have been inconsistently divided into domains, and built a version of a consistent check that can be used to perform automated error checks on manual edits. This summer, I hope to further improve the current domain identification algorithms used to build the SCOPe database by surveying and integrating suitable structural comparison program into the identification pipeline....Read More about Shiangyi Lin
Pesticides and the Public Understanding of Science"
This summer, I will continue assisting Dr. Conis on the research for her book on the history of pesticides in the United States. This entails researching and writing memos on topics ranging from pesticide poisonings of farm workers, to the link between chemical weapons and pesticide innovation, to the funding sources of pro-industry science organizations in the 1980s. Understanding how these phenomena unfolded, including who had a seat at the table, who didn’t, and who was put at risk, will be crucial if we are to protect ourselves and our planet going forward....Read More about Madeleine (Maddie) Lipscomb
Preservation of Rare Books in Republican China"
This summer, I will continue to work with Professor Volpp to recover the preservation history of a collection of rare books from the Song and Ming Dynasties, tracing their journey in wartime China before arriving at the Library of Congress. Preserving these rare books took the joint efforts of a generation of scholars and librarians from China and the U.S., while the details of this history are still a mystery. Retrieving this history allows us to reexamine this important, early cultural exchange between China and the U.S.....Read More about Tianyi Tina Liu
Analyzing the Regulatory Roots of Inequality"
Dr. Steven K. Vogel and I will be looking at how rules shape market outcomes in a variety of fields. Specifically, we will be looking at the ways formal regulations and informal practices affect inequality in areas ranging from entrepreneurship to labor markets. Through a combination of economics, political science, and political economy literature and theory, we hope to use this information to better understand the ways governments can promote more equitable outcomes....Read More about Sunny Malhotra
Using Energy Flux Potential to understand changes in the Atlantic Meridional Overturning Circulation"
This project hopes to better understand the changes to the Atlantic Meridional Overturning Circulation (AMOC) that are projected under a warmer climate and higher CO2 concentrations. We will use a variety of model simulations to analyze past and future AMOC behavior and how these behaviors shape the climate. We are particularly interested in shifts and changes to precipitation due to AMOC circulation changes and plan to use the concept of energy flux potential to constrain these changes....Read More about Paul Nicknish
Land Grabs and Legal Empowerment in Lagos, Nigeria"
This summer, I will be traveling to Lagos, Nigeria to continue research on Dr. Ferme’s project on the ways in which the large-scale acquisition of land by private actors, or “land grabs”, creates lasting implications for indigenous peoples and the “Legal Empowerment” movement in West Africa. I will be researching the market in land plots in regions surrounding the Lagos Metropolitan Area in Southwest Nigeria and working to understand ancestral land ownership and current land title registration. I will also be observing the role of international aid agencies and civil society institutions in the country to understand their relationship with their Nigerian counterparts that are currently working to use the law to empower communities in the “Legal Empowerment” movement. Utilizing historical archives, anthropological databases, and official cadastral records, I hope to establish a comprehensive understanding of the changing legal and land rights landscape in Nigeria....Read More about Victoria Osanyinpeju
Understanding the role of parental sensitivity in the development of child tooth decay"
Children living with similar resources still continue to have varying levels of oral health. How is it that some families have better oral health than others? In my summer research project, I am assessing the nutrition, oral health, and parenting practices of families with children ages 3 to 6 in Nepal. I hypothesize that there is an association between the number of children in the family with the severity of child’s tooth decay, which may be mediated by nutrition practices, oral health practices, and mother’s oral health knowledge....Read More about Amy Park
Investor Engagement and Corporate Carbon Management "
As the climate crisis comes to a head, more and more investors are engaging with corporations to push them towards better environmental performance to help limit global warming. Yet, there is inconclusive evidence on whether or not engagement actually results in greenhouse gas emission reduction in line with the 2015 Paris Agreement. My research project will use corporate data from the Carbon Disclosure Project to evaluate the carbon management quality of hundreds of fossil fuel companies, better understand what behaviors drive greenhouse gas emission reduction among fossil fuel companies, and analyze the climate financial risk associated with continued investments in fossil fuels....Read More about Rebecca Pu
Acquisition of Endothermy May Cause the Loss of Cardiac Regenerative Potential"
The summer research project will help further my understanding on factors that will affect the regenerative process of cardiomyocyte cells that would be significant in regenerative heart treatment. The project will enable me to learn how to conduct mammalian cell cultures and examine an engineered mouse strain in which the chemogenetic activation of hypothalamic thermoregulatory neurons by small chemicals, potentially induces drastic reductions of body temperature and energy metabolism like the state in torpor or hibernation. In particular, I will examine whether lowering body temperature could retain cardiac regenerative potential using this mouse model. If the analysis is correct, this would indicate the first direct evidence for the causality between the increase of thermogenesis and the loss of heart regenerative capacity....Read More about Christian Ringler
COVID-19 Youth Impact Survey"
Our team, Youth & Allies Against Homelessness (YAAH), has developed a survey to assess how Youth Experiencing Homelessness (YEH) have been affected during the pandemic. All the closures and abatement of services has made an already difficult situation significantly worse and YEH are often overlooked in addressing the needs of our unhoused community. Because of this, we are seeking to find ways to reach this population so that they can provide insight that can be used to inform meaningful policy change....Read More about Greg Ritzinger
The Role of the Basal Ganglia in Motor Learning"
Over the summer, I will design an online experiment to assess the role the basal ganglia, a subcortical brain structure, plays in motor learning. Previous literature demonstrates that the brain is able to compensate for changes in the body (e.g., fatigue) and in the environment (e.g., a windy day). Whether the basal ganglia is involved in this learning process remains elusive. To answer this question, I will create a reaching experiment that specifically probes how we strategically compensate for our movement errors. To test the role of the basal ganglia, my experiment will compare the performance of individuals with Parkinson’s Disease who have impaired basal ganglia function to the performance of controls....Read More about Lauren Schuck
Investigating the Influence of Blue Light Exposure on Myopia Development of Chicks"
Myopia or short-sightedness is an increasingly prevalent ocular disorder, which has not only been linked to a number of potentially blinding diseases, including glaucoma, but also negatively affects economics due to health care costs. Increased time outdoors appears to be at least partly protective and in recent studies, short, morning exposure to blue light has been proposed as a possible treatment to inhibit myopia progression. Notably, sunlight also includes short (blue) wavelengths. Since many blue-light blocker apps exist for electronic devices and are increasingly used with the goal of promoting better sleeping patterns at night, it is very important to better understand the relationship between blue light exposure and myopia development. During this summer, I will work on an on-going research project investigating the influence of short exposure to blue light on myopia development and the effect of the timing of exposure (morning or evening), using chicks as animal models....Read More about Elham Shoghi
Planning and Evaluation of Patient Support Corps Internships in Population Health"
In the Fall 2020 and Spring 2021 semesters, I was one of the 20 student interns of the Patient Support Corps program who served as Healthcare Navigators for a COVID-19 Hotline at the UCSF Office of Population Health and Accountable Care (OPHAC). This summer, I will continue working with clinical programs at OPHAC to identify areas where undergraduate students could help with case-finding and coaching patients with chronic health conditions. Part of my work would entail establishing relationships/pipelines for the recruitment and training of students from underrepresented backgrounds. This involves conducting an environmental scan of pre-health programs featuring students from underrepresented minorities, and developing a recruitment design to increase their involvement in our program. Throughout this research project, I would also help lay the foundation for outlining different OPHAC roles and developing task descriptions. I will document my contributions as well as any training materials which will serve as the […]...Read More about Saffanat Sumra
We are aiming to bring social justice education into the classroom through a unique medium. Storied Computing is the presentation of education through a storied game. Our game, Guaiya Means Love, draws students into a world of social justice through the means of hacking the actual source code of said game. Our goal as educators is to give POC students a medium where their creativty/engagement can shine through an impactful classroom activity....Read More about Aidan Tan