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2020 Project Proposals

URSI 2020 will run from May 27 to July 31.  Student application opens Feb 21, 2020.  Only full-time Vassar students are eligible to apply.

Anthropology

Environmental Archaeology of the NYC Watershed

April M. Beisaw (Anthropology)                 

As New York City buys up land around their 19 reservoirs, once-inhabited landscapes have become wilderness. Archaeological survey of city-owned properties documents and describes what has been taken from rural communities (natural resources and cultural sites) in order to support a distant city. Data collected is mainly geotagged photographs and GPS waypoints, whose locations are then compared to historic maps to identify past waterways/wetlands/timber stands and associate ruins with archival and genealogical data. Some excavation may occur. An URSI student is needed to assist with field data collection, laboratory processing, and report writing. Fieldwork will be 2-days a week and occur away from campus. Some weekend work may be necessary.

Prerequisites:
Applicants must be able to hike 5-miles a day on uneven ground and in the summer heat. Previous coursework in archaeology, environmental studies, or GIS is required. Preference will be given to applicants who have completed an archaeological or ecological field school or GIS coursework.

How should students express interest in this project?
Apply through URSI  - being sure to address pre-requisites/skills. The most qualified applicants will be interviewed prior to an offer being made.

This is an 8 week project running from May 27-July 17.
Simulating human evolution and development

Zachary D. Cofran (Anthropology)

Growth and development are the processes that literally make us human. Over the course of our species' evolution, these processes were modified to make us into the unique animals we are today. The fossil record provides the only direct evidence of such evolutionary changes, but this record is rather fragmentary and sparse.

This URSI project therefore adopts a “virtual,” computer-based approach to study the evolution of development. We will first use 3D models of human and non-human primate bones, to quantify shape and growth patterns. We will further use these virtual methods to reconstruct fragmentary fossils of human relatives, including 130,000 year old Neandertals from Croatia, and 2 million year old Australopithecus and 300,000 year old Homo naledi from South Africa. Finally, we will combine these virtual methodologies to simulate development in extinct species, “growing” fossil juveniles so they can be compared with adults. Students will learn state of the art methods for the study of anatomy and shape, and have the opportunity to design their own developmental simulations based on original fossil data.

Prerequisites:
The project is open to all and will include training in methods. Nevertheless, preference will go to students majoring in Anthropology, and/or who have taken Biological Anthropology courses.

How should students express interest in this project?
Students should express interest in this project directly within the URSI application, specifying both why they are interested and what relevant background they have for this specific project (e.g., courses, methods training, etc.). I will reach out to candidates after reviewing applications.

This is a 10 week project running from May 27-July 31

Astronomy

Spectroscopic variability in protoplanetary disks

Colette Salyk (Astronomy)

The URSI student will perform observational studies of planet forming regions around young stars.  In particular, they will analyze spectra of protoplanetary disks, previously obtained with the Keck telescope, to search for evidence of variability.  If found, the properties of this variability will be characterized to determine its physical cause.  A particularly exciting possibility is that there may be variability caused by the presence of a young planet in the disk.  The URSI student may also participate in scientific observations and/or outreach at the Class of 1951 observatory.

Prerequisites: 
Students should have taken ASTR 220 and ASTR 230.  Preference will be given to students who have also taken ASTR 240 and/or ASTR 330.

How should students express interest in this project? 
All interested students should send me an email, so we can discuss the project in person.

This is a 10 week project running from May 27-July 31

Biology

Dissecting the molecular mechanism of translation initiation

Colin Aitken (Biology)

Translation initiation represents one of the most important readings of the genetic code and affords cells the opportunity to control gene expression in response to cellular demands and external stimuli. The misregulation of translation initiation has been implicated in myriad human diseases, including cancer and neurodegenerative disease. Eukaryotic initiation factor 3 (eIF3) is the largest and least understood of the initiation factors that guide this process; it has been implicated in events throughout the initiation pathway and beyond. We will focus on dissecting the roles of eIF3 using genetic, biochemical, and next-generation sequencing approaches. In particular, we will concentrate on further understanding the role eIF3 plays in loading the mRNA to be translated onto the ribosome. To this end, we will attempt to express and purify recombinant eIF3 from bacterial cells, enabling us to make specific mutations in eIF3 — guided by recent high-resolution structural models — and then observing the effects of these mutations within a yeast in vitro reconstituted system and potentially at the whole genome level. Additionally, we will to investigate the effects of eIF3 mutations on the translation of mRNAs in living cells. Students working in the lab will gain experience with molecular biology, protein expression and purification, biochemical and biophysical approaches, and next-generation sequencing tools.

Prerequisites:
Introductory biology and either one of the following 200-level courses (BIOL 218, BIOL 238, BIOL 244, or BIOL/CHEM 272) OR previous laboratory experience.

How should students express interest in this project?
Interested students should write briefly in their application why they are interested in this project and describe any previous experience that might particularly prepare them for it. After reviewing the applications, I will contact short-listed candidates about setting up an interview. Students should not contact me directly.

This is a 10 week project running from May 27-July 31
CRISPR/Cas9-mediated mutagenesis of the SUMO system in the moss Physcomitrella patens

Robert  Augustine (Biology)            

Small Ubiquitin-related Modifier (SUMO) is a post-translational modification that is rapidly attached to target proteins within minutes of exposure to heat, cold, and drought and acts to mitigates the damage inflicted by these stresses.  How and why are still unknown.  This project aims to take a genetics approach to understand the role of the SUMO system in the moss Physcomitrella patens.  The project will involve generating knockout mutants of SUMO genes and machinery involved in its conjugation to target proteins.  The interested student will use molecular biology techniques to generate constructs that enable the CRISPR/Cas9-mediated disruption of SUMO genes, transform them into plant cells, and screen for and characterize the resulting mutants.

Prerequisites:
Preference will be given to students with lab experience, and who have taken courses with emphasis on Cell and Molecular Biology, Genetics, Biochemistry, and/or Plant Physiology.

How should students express interest in this project?
Interested students should briefly explain why they are interested in this research topic, and how it fits into their future goals. After reviewing applications, I will set up an interview with a short-list of compatible candidates, and then select from that group.  Students should not contact me directly.

This is an 8 week project running from May 27-July 17.
Identifying the mechanisms of SUMO homeostasis in the moss Physcomitrella patens

Robert  Augustine (Biology)

Small Ubiquitin-related Modifier (SUMO) is a post-translational modification that is rapidly attached to target proteins within minutes of exposure to heat, cold, and drought and acts to mitigates the damage inflicted by these stresses.  SUMO appears to be under tight transcriptional control that prevents its hyper-accumulation, however the mechanism that regulates this homeostasis is unknown.  This project aims to characterize this phenomenon in the moss Physcomitrella patens, and develop strategies to ascertain the factors(s) that mediate this response.  This project will utilize molecular biology techniques, and there will be considerable latitude in developing strategies to identify the regulatory mechanism.

Prerequisites:
Preference will be given to students with lab experience, and who have taken courses with emphasis on Cell and Molecular Biology, Genetics, Biochemistry, and/or Plant Physiology.

How should students express interest in this project?
Interested students should briefly explain why they are interested in this research topic, and how it fits into their future goals. After reviewing applications, I will set up an interview with a short-list of compatible candidates, and then select from that group.  Students should not contact me directly.

This is an 8 week project running from May 27-July 17.
Metagenomic analysis of Capsicum spp dietary intervention sequences

Funmilola Ayeni (Biology)

Pepper (Capsicum spp) is a significant plant of the Solanaceae family, often regarded as one of the earliest spice used by humans. The frequent consumption of pepper in humans has been noted to result in gastrointestinal upset and other side effects. The momentary diarrhoea has been attributed to the irritation of the digestive system (stomach and intestinal linings) by Capsaicin, a potent ingredient in chili peppers which triggers certain receptors in the digestive system, resulting in burning sensation followed by rapid and hence inadequate processing of the food.

While the effect of pepper and hence Capsaicin on the physiology of the body is adequately understood, there is lack of information on the effect of its consumption on the human gut microbiota. Hence, there is need to understand the impact of its consumption on the quantity and composition of microorganisms in the gut. We hypothesize that dietary intervention with pepper in human volunteers will lead to changes in the composition and proportion of the intestinal microorganisms. Metagenomic sequences already obtained from 16S amplicon sequencing of extracted DNA  from volunteers` faecal samples will be analyzed with QIME2 software and different bioinformatic analysis will be done on them.

Prerequisites: 
1. Bioinformatics courses.   2. Ability to familiarize, learn and use new bioinformatics software and command lines

How should students express interest in this project?  
Interested students should send mail directly to fayeni@vassar.edu

This is a 10 week project running from May 27-July 31

Restoration, ecological management and land use history on the Ecological Preserve

Keri VanCamp (Director of the Ecological Preserve), Margaret Ronsheim (Biology), April Beisaw (Anthropology)

The Vassar Ecological Preserve is implementing a Conservation Action Plan to manage the threats its ecological communities are facing in a changing climate.  The characterization of the ecological communities on the preserve is important for understanding the status of habitats and developing interventions to ensure that the key ecological attributes of priority communities are maintained and restored.  Many of the vegetation patterns we see on the ecological preserve are driven by its complex land use history.  This collaborative URSI project will focus on assessing the accuracy of the existing ecological communities map, mapping land use history on the preserve, and working to implement ongoing monitoring protocols that track indicators of ecological community health.  We will work to link our findings to management interventions that will improve the resiliency of communities on the ecological preserve.  Ecological restoration of priority areas on the Preserve and natural areas on campus such as the Edith Roberts Ecological Laboratory will also be conducted, including on-site propagation of native species for these restoration efforts.

Students will have the opportunity to learn a wide range of field techniques and restoration strategies. This position will provide an excellent opportunity for any student interested in pursuing conservation biology, restoration ecology, natural resource management and/or ecology as a career.

Prerequisites:
An interest in land management, restoration, ecological monitoring, and mapping is essential.  Classes such as GIS: Spatial analysis, Cartography, Ecology, Plant Diversity, Introductory Biology, and Conservation Biology would be helpful.  Applicants should have plant and animal identification skills and be able to use a dichotomous key.   The successful candidate must enjoy working outdoors, have good organizational skills, and be capable of working in adverse conditions.  Experience working with GIS/GPS and conducting research are preferred.

How should students express interest in this project?
In your application please specify if you are most interested in restoration, implementation of the Conservation Action Plan, or examining the land use history of the Preserve.  This is a collaborative project among Keri Van Camp (Director of the Ecological Preserve), April Beisaw (Anthropology), and Meg Ronsheim (Biology) and we will work together to build a team for this summer's project.  Once we have received all the URSI applications we will contact you to set up a time to meet.  We are also happy to answer any questions you might have during the application process.

This is a 10 week project running from May 27-July 31
Gonadotropin-like receptors in cnidarians

Jodi Schwarz (Biology)   

Corals reproduce in highly synchronized spawning events that are regulated by seasonal and lunar cycles, and which also may be regulated through detection of chemical or hormonal signals in the environment. Yet nothing is known about chemical/hormonal signals that might play roles in regulating the spawning event, nor the cell receptors that respond to those signals. In vertebrate animals, the molecular control of gamete release involves  LGR receptor proteins (Leucine-rich repeat containing G-protein coupled receptor) that function as receptors for glycoprotein hormones such as luteinizing hormone (LH) and follicle stimulating hormone (FSH). In previous work we have found that some corals and other cnidarians express LGR genes, including homologs that are closely related to receptors of reproductive glycoprotein hormones. We also have found that reproductively mature sea anemones express an LGR homolog in mesentarial tissues associated with the development of gametes. A primary goals of this URSI project will be to explore the impact of reproductive hormone exposure on anemone spawning behavior. A second goal will be to identify LGR homologs in other cnidarian species, using bioinformatic techniques, and explore the expression of those genes.

Prerequisites:

  1. Animal care: this research project depends on live animals that require daily care (1-2 hours a day M-F and occasional Saturdays). Applicants must be willing to commit to this work and to communicate/coordinate ahead of time to find a replacement in the event that they can't come in one day.
  2. Experimental sampling time points: Some experiments may require early morning or late night sampling points. Applicants must be willing to share in this responsibility and to coordinate schedules so that sampling points can be taken.
  3. Previous training: because this project involves work with live animals, molecular lab work, and bioinformatics work, applicants should demonstrate that they have received training/experience in at least two of these areas. This experience might be from a lab class. For example, if you have taken a Genetics class at Vassar, then you have received training in bioinformatics, and you should describe that training.

How should students express interest in this project?
To apply, please send an email that (1) describes your interest in this project, (2) explains how your background and experience make you a good candidate for this project, and (3) explains how you meet the pre-requisites. All applicants who meet the basic requirements will be contacted to schedule a short interview.

This is an 8 week project running from May 27-July 17.

Chemistry

Function and structure of surface-bound tau

Zachary Donhauser (Chemistry)

Tau is a neuronal microtubule associated protein with a variety of important cellular functions, most notably stabilizing and organizing microtubules in axons. Tau is also implicated in a wide range of neurodegenerative disorders including Alzheimer's disease, frontotemporal dementia, parkinsonism linked to chromosome 17 and chronic traumatic encephalopathy.  All of these diseases are characterized by abnormal aggregation of the protein. Although tau has been the focus of significant recent research, the full range of its normal functions are not understood. Tau is an intrinsically disordered protein, with functions that are generally dictated by interactions with its binding partners.  The overall focus of this project is to build a better understanding of tau’s behavior when it is in a bound state, using atomic force microscopy (AFM) as the central tool for interrogating the protein.

Prerequisites:
Introductory Chemistry and/or Introductory Biology
Recommended courses: Biochemistry, Physics

How should students express interest in this project?
Email me and set up an appointment to discuss.

This is a 10 week project running from May 27-July 31
Biochemical Characterization of Microbial Enzymes

Krystle  McLaughlin (Chemistry)        

Humans and microbes have a complex relationship. The advent of antibiotics allowed humans to fight pathogenic bacterial infections that threatened our livelihood. However, microbiome dysbiosis, the imbalance of symbiotic microbial populations in the body which can be caused by lifesaving antibiotics, has been implicated in many areas of human health. We will use biochemical and biophysical techniques to characterize proteins from various pathogenic or symbiotic microbes. These studies help to provide further understanding of essential microbial processes at the molecular level. Students working in the lab will gain experience with gel electrophoresis, protein expression and purification, in vitro enzyme assays, and protein crystallization.

Prerequisites:
Chem 125 (required)
Bio 107 (or equivalent intro bio course) and Bio 272 (preferred)
OR related previous lab work

How should students express interest in this project?
In their application, students should describe briefly 1) why they are interested in this project, and 2) how working on this project will help them reach their career goals. Students do not need to contact me directly. After reviewing the applications, I will contact selected candidates about setting up an interview.

This is an 8 week project running from May 27-July 17.
C-X Bond activation through the Oxidative Addition of Methyl Iodide to Gold(I) Trinuclear Complexes

Brooke Michelle Otten (Chemistry)

There have been previous studies on the oxidative addition of halogens to gold(I) trinuclear complexes that have shown that the oxidative addition is (1) stepwise and (2) results in a change in the oxidation state of gold from I to III. Due to the ability of the halogen substrates to be polarized, the mechanism by which this oxidative addition takes place is well understood. This project will focus on the mechanistic study of the oxidative addition of methyl iodide to gold(I) trinuclear complexes through the activation of the carbon-iodide bond. There has been experimental data to show that these reactions occur since the 1970s, but there has been no computational investigation of the mechanism of these reactions. This study aims to launch an investigation into the nature of these oxidative addition reactions and determine the mechanism under which they proceed. This will be done through the use of chemical modeling to determine the structures of the transition state as well as the oxidation number of the metal centers involved. Understanding how these reactions take place and how the properties of the gold complexes affect the reactions will lead to a greater understanding of the electronic properties of these systems.

Prerequisites:
Completion of Chem 125 and an interest in inorganic and physical chemistry. The ability to use excel effectively and general knowledge of statistics.

How should students express interest in this project?
In order to be considered for this project please send an email of interest. In the subject line please include your name and that it is in regards to URSI (i.e. – Brooke Otten – URSI). In the email please state your name, your year, your major (if declared) and what draws you to this project. Students should have an interest in material science and inorganic chemistry, as well as computational chemistry. An interest in statistical analysis and the ability to program in excel are desirable. The project will focus on computational modeling so a general knowledge of UNIX is preferred but not mandatory. Students should have completed Chem 125 or Chem 108/109 and have a general knowledge of statistics.

This is a 10 week project running from May 27-July 31

Formation and chemical functionalization of endohedral metallofullerenes

Christopher Smart (Chemistry)

Endohedral metallofullerenes are produced when graphite rods, doped with rare-earth metal oxides, are vaporized in an electric arc flame.  The exterior surface of the carbon cage of these metallofullerenes can then be modified by standard organic chemical reactions, allowing a variety of chemical functionalities to be incorporated in the molecular structure.  Our intention is to make new medicines by attaching antioxidant functionality to the fullerene surface of endohedral metallofullerenes.

The experimental work of this project will begin with optimizing and running the arc-vapor synthesis reactor to produce endohedral metallofullerenes of the desired structure.  This will include purification of product mixtures and identification of the pure compounds.  Once pure endohedral compounds are prepared, we will explore the surface chemistry of the metallofullerenes via organic reactions that are known for the surfaces of empty-cage fullerenes.  We will attempt to incorporate anti-oxidant molecular functionality by using these reactions to connect known antioxidants to the fullerene surface.  New products will be purified and characterized by standard spectroscopic techniques such as NMR, IR, UV-visible spectroscopy and elemental analysis.  We will also measure the antioxidant capacity of any new fullerene-containing compounds by standard electrochemical techniques.

Prerequisites:
Two semesters of Organic Chemistry (equivalent to CHEM 244/245) is highly recommended.  Prior research experience is NOT required.

How should students express interest in this project?
Students interested in this project should contact me by email (chsmart@vassar.edu) to arrange for a short interview with me.

This is a 10 week project running from May 27-July 31

Cognitive Science

Learned Categorical Perception Research

Janet Andrews (Cognitive Science

The purpose of this URSI project is to extend our ongoing efforts to develop a more rigorous and informative methodology for testing a phenomenon known as learned categorical perception (CP). The paradigm we are currently working with uses a psychophysical task to test participants’ ability to detect very small stimulus differences in novel visual patterns and to determine whether learning to categorize the patterns influences this ability relative to a control task that doesn’t involve learning categories, which is the learned CP claim. The work will include visualizing and analyzing data, developing further experiments, conducting experiments online, and applying meta-analytic techniques to relevant research literature.

Prerequisites:
Intermediate level coursework in cognitive science, interest in the project, and a willingness to learn and program in JavaScript and R are required; background in programming, research methods, and statistics, and prior familiarity with R, are very desirable.

How should students express interest in this project?
Students do not need to contact me with regard to their application.

This is a 10 week project running from May 27-July 31
Using Online Games to Study Human Cognition

Josh de Leeuw (Cognitive Science)

The goal of this project is to develop casual online games that contain embedded experiments investigating aspects of human cognitive performance. Using online games to study cognition has several advantages over traditional laboratory experiments, including access to a larger and more diverse pool of potential participants, better external validity of the results, and lower cost. To develop the game, the URSI fellow will read the literature to identify methodological approaches that are appropriate for gamification, develop a plan to gamify the experiment, implement the game using JavaScript, and then conduct a pilot experiment to test the validity of the experiment embedded within the game. The developed game will become part of a suite of games available online at www.thebraingamelab.org, allowing us to track how performance in different games is correlated.

Prerequisites:
Students should have some background (such as a completing a course or prior experience) in either behavioral research or programming.

How should students express interest in this project?
In the application, please clearly describe any coursework, experiences, or skills that are relevant for the project. You do not need to contact me prior to submitting the application.

This is a 10 week project running from May 27-July 31
Development of a data analytic pipeline for processing and analyzing functional brain activity

Josh de Leeuw (Cognitive Science), Hadley Bergstrom (Psychological Science), Bojana Zupan (Psychological Science), Lori Newman (Psychological Science)

Understanding brain function requires the ability to image neuronal activity and then process neuronal network computations in real time and space. Here at Vassar, we have recently developed a miniaturized microscope (i.e., the Miniscope) that allows us to peer deep inside the brain to study neuronal activity at single cell resolution and at high speed. This technology produces terabytes of data, creating challenges in both data processing and data analysis. This URSI project will1) develop a processing pipeline to extract signal from raw imaging using high-performance computing resources, and 2) begin to develop a set of data analytic tools using machine learning to decode the relationship between brain activity and behavior.

Prerequisites:
Experience or interest in programming, data science, big data, machine learning, neuroscience, psychology, and/or cognitive science is preferred. The project will involve working with a team that will include fellow URSI students and faculty, so we encourage students who have some but not all of the relevant experience or interests to apply.

How should students express interest in this project?
Please clearly describe in your application any experiences that you feel are relevant to the project. You do not need to contact us prior to submitting an application. We will reach out to students for interviews after the applications are in.

This is a 10 week project running from May 27-July 31
Evolutionary Developmental Robotics

Kenneth Livingston (Cognitive Science

This project will continue research in our laboratory that uses real and simulated robots to study basic principles of evolutionary change as they affect agent intelligence.  Factors being explored include (1) characteristics of the genotype-to-phenotype mapping system, (2) contributions of epigenetic and developmental processes, and (3) the contributions of agent morphology and environment.  The work will involve construction and maintenance of simulations and real robots, collaboration in hypothesis generation and experimental design, and all phases of data collection and analysis.

Prerequisites:
Some coding experience is essential, and familiarity with the family of C-programming languages (or ability to come up to speed on them quickly) is especially desirable.  Highly desirable but not required are (a) background in statistics and experimental design and (b) a background in genetics/genomics or evolutionary theory.

How should students express interest in this project?
In addition to submitting the formal application, interested students should contact me directly to set up an appointment to discuss the project.  Final selection will be based on both the application materials and the interview.

This is a 10 week project running from May 27-July 31

Computer Science

Computational Analysis of Literature

Jonathan Gordon (Computer Science)

This project will build on URSI research that created an electronic corpus of literature annotated with biographic, geographic, and publication metadata. Using modern natural language processing and data science methods, we will design tools to explore linguistic and thematic variation in the corpus across bounds of time, space, and society.

Prerequisites:
Required: Strong programming skills and an interest in natural language processing, linguistics, or digital humanities.

Preferred: Coursework in computer science (especially CMPU 203, 240, and 366), data science, cognitive science, linguistics, or literature, and experience programming in Python.

How should students express interest in this project?
In the application, state any relevant coursework, experiences, or skills. Students don’t need to contact me before submitting an application but are welcome to email questions.

This could be an 8 or 10 week project running from May 27-July 17 or July 31.  To be determined in consultation with Prof. Gordon.
Algorithms for Temporal Networks

Luke Hunsberger (Computer Science)

A temporal network is a data structure for representing and reasoning about time, especially constraints on activities.  Different kinds of temporal networks have different kinds of features (e.g., some can accommodate actions with uncertain durations, while others can accommodate actions that generate information in real time). This project will involve implementing algorithms from the literature on Temporal Networks with the aim of empirically evaluating them in reproducible ways.

Prerequisites:
Students should have taken CMPU-101, CMPU-102 and CMPU-145.  CMPU-203 and CMPU-241 are recommended.

How should students express interest in this project?
Interested students should contact me by email (hunsberger@vassar.edu) to set up an appointment to discuss the project. Please include a summary of your prior programming experience in Computer Science.

This is a 10 week project running from May 27-July 31
Vassar College Artifacts Database

Marc Smith (Computer Science)

The Vassar College Artifacts Project (VCAP) is a college-wide effort to discover, identify, preserve, and catalog forgotten teaching artifacts from Vassar's history. The WordPress site (http://pages.vassar.edu/vcap/) contains more information about the project, as well as galleries, photographs, information, and stories about the artifacts themselves. However, the VCAP Database itself is not yet available online as it is still under development. During fall 2019 two students (Noah Ari'20 and Norman Kuang'21) in my CMPU-381 Relational Databases Intensive began work on the design, implementation, and population of this database. This effort included beginning the development of SQL queries, and working with the actual VCAP data. Noah and Norman are continuing to work on the VCAP database this spring as part of joint Senior Independent Work. I'm looking for a student to continue this effort during URSI 2020, and possibly beyond, with the eventual goal of integrating access to the VCAP database with the VCAP WordPress site. This could be a companion web application cross-linked with the existing VCAP WordPress site. Depending on how far Noah and Norman get this spring, this project will require elements of database and query design, and agile web application design, development, and testing.

Prerequisites:
CMPU-145 and CMPU-203. No prior experience with relational databases and SQL required.

How should students express interest in this project?
Students interested in this URSI project are encouraged to email me at mlsmith@vassar.edu and introduce themselves. Please let me know all the ways this project interests you and why you are applying for this project. I don't expect students applying to have any prior experience with databases, only an interest in learning about them. I don't expect students to have software development experience beyond what is covered in CMPU-203, but students who apply should genuinely enjoy software development. Finally, while I'm not asking for a commitment beyond the summer, students who are genuinely interested in the Vassar College Artifacts Project and open to the possibility of continuing to work on this project next year are especially encouraged to apply.

This is an 8 week project running from May 27-July 17.
Decentralized Policy-Based Private Analytics

Jason Waterman (Computer Science)            

Ubiquitous sensing and data collection through our personal devices and our environment have created the potential to offer innovative services and applications while creating significant value from our personal data. These data are often used for a variety of personal and public Machine Learning (ML) models, such as building targeted advertising, content recommendation, and health analytics.  Building these models present several challenges: trust, as the user requires guarantees that their provided data will not be misused by the service provider; security, as these rich data resources are valuable to criminals; and scalability, as the costs of building and maintaining large data-centers can be prohibitive.

To tackle these challenges, we are building a scalable, privacy preserving approach to personal data processing. Rather than centrally collecting data from a user population for later processing, we move the required computation to the network edge where data logically resides and can be verified to be used in accordance with a user's privacy policy. This model is a better fit for current privacy and data processing regulation and allows data subjects to bear more of the cost burden of providing storage, computation and connectivity while preserving privacy.

Prerequisites:
Strong Python programming skills are a must.  In addition, students should have already taken CMPU-203 and CMPU-224.

How should students express interest in this project?
Students interested in this project should email me to set up a meeting to discuss the project.

This is a 10 week project running from May 27-July 31

Earth Science

Climate History of the Rensselaer Plateau, east-central New York

Kirsten Menking (Earth Science)         

Earth's history of climatic change is recorded in a variety of geological and biological proxies for parameters such as temperature and precipitation. In this URSI project, we build on the work of the spring 2020 ESCI/ENST 335: Paleoclimatology senior seminar by using diatoms, pollen grains, and plant macrofossils in a sediment core collected from Dyken and/or Shaver Pond to uncover the climatic history of the Rensselaer Plateau, just east of Albany, NY. The Rensselaer Plateau hosts a number of different biological communities that are sensitive to climate change. Covered by the Laurentide ice sheet until as recently as 15,000 years ago, the Plateau has experienced several climatic oscillations, including wetter intervals and drought, that are recorded in changes in vegetation both surrounding and within the ponds. Understanding the nature of these climatic changes, what caused them, and how long they lasted is very important for our comprehension of what the climate system is capable of doing in the absence of human activities and provides the baseline against which anthropogenic climate change can be measured. In addition, some earlier intervals in Earth history may provide insights into how the vegetation on the Rensselaer Plateau will respond to future warming.

Prerequisites:
This project is best suited to students who have taken ESCI/ENST 335: Paleoclimatology, but students who have not taken this course will also be considered. Students will preferably have some familiarity and comfort with using compound and dissecting microscopes as most of the work will involve identifying and counting pollen grains, diatoms, and plant macrofossils under the microscope.

How should students express interest in this project?
Interested applicants should send an email to Kirsten Menking (kimenking@vassar.edu) expressing what about the project sounds interesting to them and why, outlining their previous experience with or enthusiasm about learning how to work with microscopes, and providing their current class schedule and suggested times for an interview.

This is an 8 week project starting 2 weeks later than other projects and running from June 8-July 31.

Mathematics and Statistics

Knot theory and arc index

Adam Lowrance (Mathematics and Statistics)           

A knot is a closed path in 3-space, and two knots are considered the same if one can be continuously deformed into the other by stretching or moving the path through 3-space. A common way to study knots is via their diagrams, i.e. projections of the path in 3-dimensions to a picture in the plane. The fewest number of crossings in any diagram of a knot is a natural measure of complexity on knots. Another way to study knots is via their grid diagrams, square grids where segments of the knot diagram are parallel to the coordinate axes. The smallest size of any grid for which a given knot has a grid diagram is another natural measure of complexity on knots called the arc index of the knot. In this project, we will compare these two different measures of complexity for specific families of knots.

Prerequisites:
Required prerequisite: Math 220 and Math 221. Useful (but not required): some proof-writing experience.

How should students express interest in this project?
Students should email me to set up an appointment to discuss the project in more detail.

This is a 10 week project running from May 27-July 31

Physics

Ultrafast laser science at the nanoscale

Brian Daly (Physics)          

Ultrafast lasers produce pulses of light that are less than 1 picosecond (A millionth of a millionth of a second) in duration. These remarkable light sources allow for investigations of extremely short lived phenomena in solid materials. Of particular interest to my research group are the conduction of heat and the propagation of ultrasound in novel nanostructures (1 nanometer is one billionth of a meter). We have several goals this summer. First, we have an ongoing project to study surface acoustic waves at their highest possible frequencies-near 50 GHz. Second, we have a collaboration with the Materials Science department at Penn State University to create and study thin solid layers that can be as thin as a single molecule and have interesting optical and electronic properties.  Finally, we are also continuing a computational modeling study of the interaction of light waves and vibrational waves in nanostructures. Four positions are available; two students will work here at Vassar and two will have the opportunity to work at the 2D Crystal Consortium Materials Innovation Platform, a NSF national user facility https://www.mri.psu.edu/mip.

Prerequisites:
One year of physics and mathematics is required. PHYS 200, 202/203 and MATH 220, 228 are recommended.

How should students express interest in this project?
Aside from this application, you do not need to contact me in order to express your interest in the project. I will send out emails to contact you once I have read through all the applications.

This is a 10 week project running from May 27-July 31
Study of light-matter interactions by non-conventional microscopy

Juan M. Merlo-Ramirez (Physics and Astronomy)                

The quest for faster and more efficient materials has pushed the limits of modern technology. In this sense, quasi-particles called surface plasmon polaritons (SPPs) —cumulative oscillations of the electron cloud in a conductor— have the advantage to have the same properties as electromagnetic waves and also have the quantum signature of electrons and photons. These properties allow us to use SPPs to build devices that eventually could substitute our current electronic technology and generate materials that do not exist in nature, i.e. metamaterials. In this project, we will explore the interactions between SPPs with specially designed surfaces, as well as 2D materials. The observation of such interactions will be performed by using near-field and leakage radiation microscopy, both non-conventional microscopy techniques. We will explore the existence of strong coupling between SPPs and properties of the 2D materials, and also will try to find a technological application of our results.

Prerequisites:
These are some of the characteristics a person should have for this project (any Vassar student can fulfill these requirements):
- Proactive
- Independent
- Curious
- Disciplined
Knowledge of electromagnetic and quantum theory is a plus but not a requirement.

How should students express interest in this project?
Please contact me by email. I will answer to the candidates I am interested on to arrange an interview.

This is a 10 week project running from May 27-July 31

Psychology

Visualization of a generalized memory trace in the brain

Hadley  Bergstrom (Psychological Science)   

Generalization represents the transfer of conditioned responding to stimuli that perceptually resemble the original conditioned stimulus. Generalization was noted by Ivan Pavlov in 1927, has been demonstrated across both classical and instrumental forms of conditioning, in a wide range of species (from reptiles and amphibians to birds and mammals), and has even been proposed as a universal law in the field of psychology. Despite the immense theoretical importance of generalization in the field of psychology, the nature and site of formation and storage of generalization is poorly defined. One way to study the physical representation of memory in the brain (i.e., the engram) is through genetic “tagging” technology. Genetic tagging allows for the identification and tracking of groups of neurons in the brain over time in a genetically modified mouse model. Recently, we began a transgenic breeding program to produce mice that express a Green Fluorescent Protein (GFP) reporter that is restricted to functionally defined (Arc/arg3.1) populations of neurons in the brain (ArcCreERT2). These mice permit indelible genetic access to functionally defined neurons, for the lifetime of the organism. The goal of this URSI project is to conduct a “proof-of-principle” series of experiments to verify the use of the ArcCreERT2 to visualize neurons activated in response to a conditioned stimulus, and under experimental conditions that promote generalization (the passage of time). In this way, we will have the opportunity to identify and directly compare the underlying neuronal ensemble structure of a cued and generalized aversive memory trace.

Prerequisites:
The URSI project requires interest/experience in psychological science and/or neuroscience. Courses in Introduction to Neuroscience & Behavior (Neuro 105), Research Methods in Physiological Psychology (Psyc 249), and Principles of Physiological Psychology (Psyc 241) are desirable, but not required. Basic animal handling skills, chemistry lab skills, and data analytic skills are also highly desirable. The project will involve working with a team that will include fellow URSI students and faculty. See the Memory Neuroscience Lab website for more information about our research.

How should students express interest in this project?
Please clearly describe in your application any experiences that you feel are relevant to the project. You do not need to contact me prior to submitting an application. I will reach out to students for interviews after the applications are in.

This is a 10 week project running from May 27-July 31

Astrocytes in cognition: Potential targets for neurodegenerative diseases

Lori Newman (Psychological Science)

Over the last century, the role of neurons in communicating information has been the focus of the majority of neuroscience research due to their unique electrical capabilities allowing for easy analysis of their activity. The other cells in the brain, known as glial cells were mostly thought of as support for the neurons, literally deriving their name from the Greek for glue, as they were merely thought to hold the brain together. Recently, a focus on the role of glial cells, particularly astrocytes in brain function has begun to emerge as a potential new target for therapeutics after finding that subtle manipulations of astrocytic function can greatly affect learning and memory (Newman, Korol & Gold, 2011). The purpose of this URSI project is to understand the basic science behind the role of astrocytes in providing metabolic resources during cognition. Using pharmacological manipulations specific to astrocytes, we will explore what effects manipulation of glycogen breakdown has on executive function. This project is ongoing and is expected to span multiple semesters.  Students interested in neuroscience, medicine, or psychology are encouraged to apply.

Prerequisites:
Experience working with animal models is preferred.

How should students express interest in this project?
Please clearly describe in your application any experiences that you feel are relevant to the project. You do not need to contact me prior to submitting an application. I will reach out to students for interviews after the applications are in.

This is a 10 week project running from May 27-July 31
Measuring glutamate recycling in astrocytes with a miniature fluorescent microscope

Lori Newman (Psychological Science)

In the field of neuroscience, some measure of activity in the brain is required for unraveling complex relationships between the brain and behavior. While neurons have clear electrical signals with activity that can be measured, astrocytes do not.  Due to this difference, the study of the role of astrocytes in behavior in real time has been lacking.  This past semester we have begun using miniscopes, or miniature microscopes, to visualize glutamate uptake into astrocytes by inserting fluorescent glutamate sensors into astrocytes in rats, a novel technique as previous published research has focused on miniscope use in mice (Resendez et al., 2016).  Glutamate is the major excitatory transmitter in the brain and recycling glutamate through the astrocytes promotes distinct and accurate neurotransmission in the brain.  The purpose of this URSI project is to continue to assess how these glutamate recycling dynamics change in vivo with cognition. Students interested in neuroscience, psychology, engineering, physics, mathematics or computer science are encouraged to apply.

Prerequisites:
Experience working with animal models is preferred.

How should students express interest in this project?
Please clearly describe in your application any experiences that you feel are relevant to the project. You do not need to contact me prior to submitting an application. I will reach out to students for interviews after the applications are in.

This is a 10 week project running from May 27-July 31
Mental Health in Refugee Populations

Sue Trumbetta (Psychological Science)Maria Höhn (History)        

As part of a multi-year project with the Consortium on Forced Migration, Displacement, and Education’s (CFMDE), ideally, two Vassar URSI students will conduct empirical research on mental health among forcibly displaced populations.  Students will work with Professor Adam Brown and his graduate students in the Trauma and Global Mental Health Lab at the New School for Social Research (New York City) during the first part of the summer (4-6 weeks).  This work will introduce students to some of the databases and data analytic techniques necessary to their URSI research.  The second part of the summer’s work will take place in Bern, Switzerland.  In Bern, students typically spend mornings in data analysis and/or didactics in mental health and research methods, followed by afternoon visits to clinics at the University Hospital and to community organizations, eventually helping to conduct the research.  Professor Brown has at least two ongoing studies: a study of migration-related stressors, anxiety, and trauma in asylum-seekers who come to the hospital Emergency Department, and a study of how partnerships between the University Hospital and community organizations may effectively reduce the number of Emergency Department visits.

Please note that this URSI project is slightly different from typical ones as you will be away from Vassar's campus (in New York and Bern).  In order to defray that cost, the student will receive $2000 in supplemental funding through The Andrew W. Mellon Foundation to cover room and board to make the award equitable with the existing URSI model.

Prerequisites:
PSYC 200 or other Statistics course strongly preferred.  Command of a language other than English strongly preferred.

How should students express interest in this project?
After a review of applications, Vassar advisors Professor Susan Trumbetta (Psychological Science) and Professor Maria Höhn (History; Director of CFMDE) will select and contact students for interviews; students will also interview with Professor Brown.

This is a 10 week project running approximately from May 27-July 31, but may vary.
Quantification of oxytocin receptors on GABAergic interneurons in the mouse VTA

Bojana  Zupan (Psychological Science)

The mouse model of Fragile X Syndrome (FXS), the largest single-gene cause of autism, recapitulates many autism-related behaviors including abnormal sociability, a core symptom of many neurodevelopmental disorders. Our lab has shown, however, that genetically unaffected mice derived from fmr1-deficient females also show behavioral abnormalities, specifically increased sociability, suggesting that reduction in maternal fmr1 expression has an intergenerational programming effect on offspring neurodevelopment. Sociability is modulated in part by oxytocinergic (OXTergic) signaling in the ventral tegmental area (VTA), and while intranasal OXT increases social approach in control mice, those programmed by maternal fmr1 deficiency show reduced social approach following OXT administration. Reduced sensitivity to OXT may be due in part to altered expression of OXT receptors (OXTRs) in the VTA, which are found on both dopaminergic and GABAergic neurons. As our previous data suggests no differences in OXTR expression on dopaminergic neurons, this project will assess OXT receptor expression levels specifically on GABAergic interneurons of the VTA using an already established protocol for fluorescent in situ hybridization (FISH). This project will involve animal handling and sample processing (wet lab), confocal microscopy, and image analysis (ImageJ).

Prerequisites:
Previous rodent handling and research experience as well as successful completion of Research Methods in Physiological Psychology preferred.

How should students express interest in this project?
Please describe in your application any research interest and/or experience you feel may be relevant to this project. Please do not email Prof. Zupan prior to submitting the application. Students will be contacted for interviews once all applications are submitted.

This is a 10 week project running from May 27-July 31
Visualization of VTA DAergic neural activity during social behavior in mice

Bojana  Zupan (Psychological Science)

Social behavior is modulated in part by activity of dopamine (DA) neurons in the ventral tegmental area (VTA). Specifically, DAergic projections to the nucleus accumbens (NAc) bidirectionally modulate duration of social interaction: increased DAergic activity increases social interaction time while decreased neural activity decreases time spent with a novel same-sex conspecific. Our lab has found that maternal fmr1 deficiency (a mouse model of Fragile X Syndrome, largest single-gene cause of autism) programs social behavior, possibly by altering DA neuron activity in the VTA. Electrical activity of neurons is accompanied by rapid changes in intracellular calcium levels, which can be detected in vivo using fluorescently-labeled calcium sensors and miniscope technology (see G. Coste URSI 2018 project). This project is a continuation of ongoing work in the lab that aims to determine whether maternal fmr1-dependent changes in sociability are indeed associated with dysregulated activity of DAergic neurons in the VTA.  The project will involve extensive animal handling, behavioral testing, and data processing. Opportunity to perform surgical manipulation and tissue harvest will depend on candidate’s degree of experience/comfort with invasive procedures.

Prerequisites:
Previous rodent handling and research experience as well as successful completion of Research Methods in Physiological Psychology preferred.

How should students express interest in this project?
Please describe in your application any research interest and/or experience you feel may be relevant to this project. Please do not email Prof. Zupan prior to submitting the application. Students will be contacted for interviews once all applications are submitted.

This is a 10 week project running from May 27-July 31