Undergraduate Research Profiles

From the class of 2011…

jeremy Jeremy Bancroft Brown

Undergraduate Student: Class of 2011
Major: Physics
Hometown: Amherst, Massachusetts
Awards (HS): National Merit Commended Student
Awards (Univ): Dean's List, Phi Beta Kappa, Class of 2011 Student Marshal, Grainger Senior Scholarship (physics)
Research: Computer-aided Diagnosis, Atomic Theory
Research Advisors: Maryellen Giger, Lorenzo Curtis and David Ellis (Toledo)

Since October 2008, I have worked as a student researcher for Maryellen Giger, Ph.D. within the Department of Radiology and the interdisciplinary Graduate Programs of the Committee on Medical Physics. My research with Professor Giger is focused on computer-aided diagnosis (CAD) for a medical imaging modality known as dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). In recent years, DCE-MRI has become a widely used clinical tool for cancer diagnosis. In particular, it is used for surgical staging of newly diagnosed cancer, evaluation of cancer treatment, and screening of patients with known risk factors for developing cancer. At the University of Chicago, physicians most commonly employ DCE-MRI to diagnose and investigate carcinomas of the breast and prostate.

A DCE-MRI exam involves the acquisition of a three-dimensional image series over time (i.e., 4D data). During the exam, a pre-contrast 3D image series is first obtained. After this, the patient receives an intravenous dose of a paramagnetic contrast agent, and additional 3D images (with approximately millimeter spatial resolution) are subsequently acquired at multiple time points. The contrast agent reduces the longitudinal relaxation time (T1) of its surroundings, and can therefore be visualized by selecting a MRI pulse sequence that weights the image contrast towards the T1 values of the patient’s tissues. Additionally, because the contrast agent is initially localized to the blood pool, it primarily circulates to well-perfused areas of the body. This attribute is diagnostically useful, because tumors tend to be highly vascularized. Moreover, invasive cancers typically exhibit a disorganized, “leaky” vasculature (due to angiogenesis) that produces a characteristic rapid uptake and rapid washout of the contrast agent. In comparison, benign cell proliferation processes generally present with slower contrast uptake and washout.

In current clinical practice, radiologists are able to extract useful information from DCE-MRI examinations, and they routinely incorporate this information into cancer diagnosis and treatment decisions by collaborating with surgeons, oncologists, and pathologists. However, there is substantial room to improve the interpretation of DCE-MRI data. A typical DCE-MRI dataset comprises 6 to 50 timepoints each containing 60 to 200 image slices, which are each composed of at least 215 voxels. This large quantity of digital data is ideally suited to computerized analysis methods. The primary goals of CAD research for DCE-MRI in Professor Giger’s lab include accurate tumor detection, delineation, and characterization to aid doctors in biopsy and treatment decisions, as well as to extract quantitative information related to patient phenotypes, prognoses, and responses to therapy. The methods used combine machine learning (neural networks and artificial intelligence) techniques with knowledge of the NMR physics and pathophysiology that underlie the data.

My own research focus within Professor Giger’s lab has been on understanding kinetic patterns of contrast uptake and washout in DCE-MRI exams. One project that I have contributed to uses a pattern recognition algorithm known as fuzzy C-means (FCM) in order to identify characteristic kinetic behavior from a given tumor. Another strategy that I have investigated involves summarizing the four-dimensional (spatial and temporally indexed) DCE-MRI data using three-dimensional (spatially indexed) kinetic feature images, which can then be analyzed using fractal dimension formalisms and higher-order texture statistics. A third thrust of my research entails comparing these population data-driven image analysis techniques to methods that extract quantitative physiologic parameters from the DCE-MRI data using pharmacokinetic models. This research requires some use of computer simulations, but it relies heavily on retrospective clinical data from hundreds of patients. My research in Professor Giger’s lab has been supported by an American Association of Physicists in Medicine (AAPM) Summer Fellowship, a University of Chicago Biological Sciences Collegiate Division (BSCD) Summer Fellowship, and Professor Giger’s research grants from the National Cancer Institute (NCI) and the Department of Energy (DOE).

During the summer of 2008, I participated in the National Science Foundation (NSF) Research Experience for Undergraduates (REU) program at the University of Toledo under the guidance of Larry Curtis, Ph.D. and David Ellis, Ph.D. In my project there, we used a semi-empirical method to characterize the 3s23p2–3s3p3 J=2 transition array in singly-ionized phosphorous (P II). In this method, Slater, spin-orbit, and radial parameters were fitted to experimental energy levels in order to obtain a description of the array in terms of LS-coupling basis vectors. The various intermediate coupling (IC) and configuration interaction (CI) amplitudes resulting from this model were then used to predict the branching fractions of transitions within the array. It was then possible to compare the semi-empirical predictions to branching ratios measured using beam-foil spectroscopy at the Toledo Heavy Ion Accelerator (THIA) laboratory. This research was motivated by the fact that P II is common in interstellar clouds. Thus, precise laboratory measurement of its energy levels and oscillator strengths (together with theoretical modeling of those quantities in order to guide and inform the experimental work) facilitates quantification of its abundance. This knowledge in turn allows astrophysicists to better understand the chemical evolution of galaxies.

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caitlin Caitlin Lanni

Undergraduate Student: Class of 2011
Major: Physics
Hometown: Pittsburgh, Pennsylvania
Awards (HS): Society of Women Engineers High Honor Award
Awards (Univ): National Merit Scholarship, Dean's List
Research: Magnetic nanomaterials, Cosmology, Geophysics
Research Advisors: Sara Majetich (Carnegie Mellon), Bruce Winstein, Dion Heinz

Although I was certain of my choice to be a physics major, throughout my time as an undergrad here I have been uncertain about which area of physics I’d like to pursue in the future. Consequently, my research positions have been rather varied because I wanted to gain experience in different fields and have a broader sense of current research topics in physics.

My first position was with Dr. Sara Majetich in the Department of Physics at Carnegie Mellon University. Our project consisted of studying the behavior of uniform magnetic nanoparticles and how they may be maneuvered using externally applied magnetic fields; the overall intention was to show that the particles could be moved in a controlled manner that would not be overwhelmed by their thermal motion in solution, and that they could theoretically be steered within living cells as a possible biomedical application. Because the nanoparticles were attracted to each other, a variety of different surfactants were applied to discourage aggregation; to determine which of these was most effective at maintaining separate, single nanoparticles rather than clusters of them, one of my responsibilities was to determine the particle size distributions of various batches of nanoparticles using both variable- and fixed-angle dynamic light scattering instruments. I was also responsible for constructing a small electromagnet capable of being mounted on a microscope stage and for using fluorescence and dark field microscopy to study the controlled motion of the particles; by capturing video of the particles both with and without the magnetic field, it was possible to show that the motion due to the applied field gradient was of several orders of magnitude larger than that which was due to the Brownian motion. Because of my contributions to the project, I’m a co-author on the Majetich group’s upcoming publication “Magnetophoresis of Nanoparticles” in the ACS journal Nano Letters.

Having delved into cosmology during a high school internship, I returned to that area during my second research position with Dr. Bruce Winstein in the Kavli Institute for Cosmological Physics, here at UChicago. His group, which collaborates with many others on the Q/U Imaging Experiment (QUIET) project, makes high-sensitivity measurements of the polarization of the CMB using coherent correlation polarimeters, a relatively recent technological development from JPL. The ongoing goal of QUIET is to analyze the polarization data in its E and B components to gain unprecedented information about the early universe and phenomena like gravitational waves. In the time that I worked with the Winstein group, the research consisted entirely of data analysis; I contributed a script to a pre-existing analysis program that allowed the user to identify particular telescope scans with excess signal in a specific frequency range. Though I found the research very fascinating, the lesson I came away from that position with was that I wanted to work in a field where experimentation is done by hand, in person, right there in the laboratory – not one where experimentation consists of receiving data from elsewhere and manipulating it on a computer.

My third (and current) research position is here at UChicago, with Dr. Dion Heinz in the Department of Geophysical Sciences. Using the simple yet surprisingly powerful technology of the diamond anvil cell (DAC) and a laser heating system, it is possible to subject materials (such as iron) to outer core conditions, over 1 million atmospheres of pressure and up to 6,000 Kelvin. Achieving these extreme conditions in the laboratory allows the measurement of various phase transformations as a function of temperature and pressure; this permits characterization of the Earth’s core that would be impossible otherwise. At the moment, we are working on a setup that makes use of a Fabry-Perot interferometer, a high-resolution instrument capable of resolving Brillouin peaks. Since Brillouin scattering occurs as a result of optical density variations arising from acoustic modes, we hope to use this method to measure elastic constants of materials at high pressure and temperature to learn more about the outer core. This experimental method has never before been used on molten metal – as a preliminary step, we are working to demonstrate its efficacy first on water and then liquid mercury.

Though my research experience may seem scattershot, I have gained a broad variety of laboratory skills, experience with particular scientific instruments and methods, and a heightened level of confidence working with hazardous or delicate equipment. No matter how you plan to apply your physics education in the years to come, gaining research experience now is a fantastic way to meet mentors and peers with similar interests and to better yourself as a student and scientist.

Publications:

JitKang Lim, Caitlin Lanni, Eric R. Evarts, Frederick Lanni, Robert D. Tilton, and Sara A. Majetich, "Magnetophoresis of Nanoparticles," (to appear in ACS Nano).

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