2021 University of Chicago Undergraduate Research Symposium: Session 2

-7/del7q Acute Myeloid Leukemia (AML) is a high-risk leukemia that accounts for about 8% of all AML patients, often resulting in a poorer prognosis as many generalized therapy methods such as chemotherapy are rendered ineffective. As the prognosis of myeloid leukemia patients remains poor, a need for targeted therapies which prove lethal to a select group of cells is needed in order to create a more effective and less toxic therapy. One approach is to identify essential genes on chromosome 7 which correlate to increased efficacy of particular drugs when expressed at haploinsufficient levels. Using previously published genome wide CRISPR-CAS9 knockout screen data conducted in AML cell lines, we identified 239 essential chromosome 7 genes in AML cell lines and further narrowed this list to 44 genes which can be targeted by a commercially available drug based on data collected from Drug-gene Interaction Database (DGIdb) and DrugBank. After identification, drug screening data performed in AML cell lines from the Genomics of Drug Sensitivity in Cancer (GDSC) database as well as drug screening data from AML patients in the BEAT AML database were utilized to verify if low expression of the target genes correlated with a difference in drug sensitivity through measured AUC values. Of the essential genes on chromosome 7 with a potential drug candidate, Bortezomib, a drug targeting proteasome subunit PSMA2, and Palbociclib which targets cyclin dependent kinase CDK6, hold potential of being more efficient in inhibiting cell proliferation in patients with -7/del7q karyotypes. These findings encourage the expansion of research for these drugs in relation to AML potentially through AML xenograft mouse models, and highlight the importance of characterizing genetics vulnerabilities in specific cancer types.

Anjali Kotamarthi

Prof. Megan McNerney, Pathology; Dr. Madhavi Senagolage, McNerney Lab

Biological & Health Sciences

Recent advances in immune checkpoint inhibitors (ICI) have revolutionized the cancer therapy landscape, improving survival in subsets of patients across a range of malignancies. However, the responses have been very limited in advanced prostate cancer (PC), due to multiple mechanisms of intrinsic resistance to ICI. One of the central mechanisms for resistance to ICI in PC is a sparse immune infiltrate, with a predominance of myeloid suppressive cells within the tumor microenvironment. We hypothesized that activation of the nucleotide-binding domain (NOD)-like receptor protein 3 (NLRP3) inflammasome can activate innate immunity within myeloid suppressive cells, thereby overcoming intrinsic resistance to ICI. We evaluated the impact of an NLRP3 agonist (BMS-392959) in a murine c-myc-driven prostate cancer mouse model. Our results demonstrate significant tumor control in BMS-392959 treated mice, which is accompanied by a global increase in immune cell infiltration. Mechanistic studies reveal a tumor extrinsic, macrophage mediated anti-tumor response driven by M1 polarization and subsequent tumor phagocytosis. Collectively, our results demonstrate NLRP3 as a promising therapeutic target to overcome resistance to ICI in advanced PC.

Anna Argulian

Prof. Akash Patnaik, Medicine, Hematology/Oncology; Dr. Kiranj Chaudagar, Patnaik Lab; Dr. Srikrishnan Rameshbabu, Patnaik Lab

Liew Family Research Fellow

Biological & Health Sciences

Multiple Sclerosis (MS) is a neurodegenerative autoimmune disease in which the immune system attacks neuron myelin sheaths in the brain. MS often leads to physical disability due to lowered communication efficiency between brain and body. During MS attacks, immune control declines, along with dysregulation of interferon-ß (IFN-ß), an antiviral signaling protein. IFN-ß therapy, the first approved MS therapy, reduces attacks, delays disease progression, and corrects abnormal IFN-ß signaling in Relapsing-Remitting MS (RRMS), the most common disease form. However, most RRMS patients eventually develop secondary progressive MS (SPMS), and the benefits of IFN-ß treatment are then diminished. We studied the IFN signature and therapeutic responses in RRMS and SPMS. We hypothesized that changes in this signature would allow us to differentiate between SPMS and RRMS and find therapeutic targets for SPMS treatment. Blood samples were from 59 patients from 6 groups of treated and untreated MS and controls. We visualized and investigated differential gene expression in immune cells, using a range of bioinformatic tools, including Transcriptome Analysis Console, Ingenuity Pathways Analysis, and Gene Ontology. Serum levels from Luminex multiplex of 78 proteins were correlated and compared. In untreated patients, gene and protein data suggested that SPMS is more ordered or quieter than RRMS, despite being more progressive, in both global gene expression and in specific pathways that regulate immune cell infiltration through the Blood Brain Barrier. We suggest this is due to recovery of aberrant gene signaling from regulatory and repair mechanisms in the transition from RRMS to SPMS. In SPMS, we detected short- and long-term effects of IFN-ß therapy and suppression of pro-inflammatory pathways and upregulation of multiple anti-inflammatory, antioxidant genes. These findings suggest new biomarkers for SPMS as well as important pathways for developing future MS therapies.

Avi Fogel

Prof. Anthony Reder, Neurology; Dr. Xuan Feng, Reder Lab

Biological & Health Sciences

The body plan of the ray-finned fishes (Actinopterygii) has undergone considerable change throughout their evolutionary history. The positioning of their paired (pectoral and pelvic) fins are no exception to this: more evolutionarily derived actinopterygians tend to have pectoral fins that are shifted upwards on the body combined with pelvic fins that are shifted forwards and closer to the pectoral fins. Mapping these changes through quantitative anatomical analysis is crucial for understanding the evolutionary significance and functional consequences of these differing fin positions. We investigated a possible mechanism for this aforementioned forward shift in the pelvic fin by determining whether anatomical changes in the bony girdle supporting the pelvic fins correlated with positional shifts in the fin itself across numerous actinopterygian families. We measured pelvic fin position relative to the pectoral fin by using R to place landmarks at key locations on images of fish, which the script would output as XY-coordinates used for computing distances. Different pelvic girdle characteristics (such as girdle plate length relative to body length, etc.) were measured on X-ray images of fish using image measuring software. We then conducted statistical analysis using Spearman’s rank correlation to determine whether these different pelvic girdle measurements were correlated with forward shifts in pelvic fin position. Of the pelvic girdle characteristics chosen, we found that a more raised anterior end and a sharper angle of pelvic girdle inclination relative to the midline of the body were indeed significantly correlated with a more forward-shifted pelvic fin. We suggest that the elevated anterior attachment of the pelvic girdle permitted attachment to the pectoral girdle, thereby stabilizing the forward shift of the pelvic apparatus.

Elisabeth Incardona

Prof. Michael Coates, Organismal Biology and Anatomy; Stephanie Sang, Organismal Biology and Anatomy

College Summer Research Fellow, Hoeft Awardee

Biological & Health Sciences

COVID-19 is an infectious disease caused by the novel 2019 coronavirus that usually presents as a respiratory illness with a range of severity and symptoms, such as pneumonia, trouble breathing, acute respiratory distress syndrome, and death. Currently, the main treatment for severe COVID-19 patients is corticosteroid administration. However, corticosteroids should be used sparingly, as they may cause serious detrimental side effects. Thus, this study aims to provide quantitative analysis of CT scans acquired from COVID-19 patients and utilize this understanding to inform treatment decisions and thus improve patient management and clinical outcomes. To accomplish this, the lung and COVID-19 involved tissue were manually segmented CT scans using the MATLAB Image Labeler by a student and experienced radiologist, respectively. The segmentations were then used to train, validate, and test a deep learning model to rapidly and consistently segment CT scans and extract quantitative imaging features such as the ratio of diseased (COVID-19) tissue to total lung tissue and intensity-based radiomic features within the diseased tissue region. The chosen model was a two-headed U-Net architecture, which takes a single slice from a CT scan as input and automatically identifies image pixels that represent the lungs as well as areas of COVID-19 involvement. The segmentation model performance will be evaluated with the Dice similarity coefficient, which compares the overlap of the model’s automatically produced lung and COVID-19 involved tissue segmentations to those provided manually. The quantitative features extracted from the segmentations will be utilized to create a model for determining optimal patient treatment options between multiple corticosteroids (dexamethasone, methylprednisolone) as well as determine COVID-19 severity, monitor response to treatment, and predict long-term dysfunction. Thus, successful application of this approach has significant implications in both clinical care and resource management.

Elise Katsnelson; Beatrice Katsnelson

Prof. Maryellen Giger, Radiology; Jordan Fuhrman, Committee on Medical Physics, Radiology

College Research Fellow (Global Health)

Biological & Health Sciences

Captive specimens in natural history collections allow researchers to inspect the morphologies of rare taxa, but the lifestyles, diets, and lifespans of captive animals differ from those of their wild counterparts. We compared bone microstructure of trunk vertebrae in captive and wild xenarthran mammals (sloths, armadillos, and anteaters). Because trabecular bone architecture (TBA) adapts to in-vivo forces, bone microstructure reflects ecology and behavior, but this means that it may differ between captive and wild specimens of the same species. We collected µCT scans of the last six presacral vertebrae in 13 species of fossorial, terrestrial, and suspensorial xenarthrans ranging in body mass from 120g (Chlamyphorus) to 35kg (Myrmecophaga). For each vertebra, we measured bone volume fraction (BVF); trabecular number (TBN) and mean thickness (TBTH); global compactness (GC); and cross-sectional area (CSA). Wild specimens generally have more robust trabeculae, but this differs based on species, vertebral position, ecology, and pathology. The wild specimens of fossorial taxa (Dasypus) have significantly more robust trabeculae than their captive counterparts, but there is no clear difference in TBA of wild and captive specimens in suspensorial taxa (Bradypus and Choloepus). These data suggest that locomotor ecology affects the level to which captivity affects bone microstructure. Captive specimens of both Tamandua and Myrmecophaga have higher BVF and TBTH than their wild counterparts, indicating more brittle trabeculae due to bone pathologies caused by captivity. Our results add to the understanding of variation in mammalian bone microstructure and suggest caution when including captive specimens in research on TBA.

Ellie Zack

Dr. Kenneth D. Angielczyk, Committee on Evolutionary Biology, The Field Museum of Natural History; Dr. Stephanie M. Smith, The Field Museum of Natural History

Dean's Fund for Undergraduate Research Awardee

Biological & Health Sciences

Individuals with psychotic disorders such as schizophrenia are thought to be disproportionately affected by substance misuse disorders. It has been found that the rate of comorbid substance abuse with schizophrenia is 3x higher than in the general population. The significance of this observed relationship is not comprehensively understood. I was awarded the Hoeft Grant to explore the complicated dynamic between substance abuse and psychotic disorders. The first step was to assess substance abuse prevalence across novel categories of psychosis experimentally created previously on the basis of neurobiological similarity. The novel categories are called “biotypes,” which are novel groupings of psychotic disorders that utilize multimodal biomarkers to define their membership, providing an alternative to current diagnostic groups (schizophrenia, schizoaffective, bipolar). I am currently comparing substance abuse prevalence between diagnostic groups and biotypes to determine whether substance misuse is differentially prevalent among the two subgrouping systems and will move on to analyze cognitive test performance in relation to these findings. I am analyzing a large amount of subject data collected by the Cognition Emotion Neuroscience Laboratory at the University of Chicago, along with four other sites across the US, for the Bipolar Schizophrenia Network on Intermediate Phenotypes study. I am focusing my analysis on variables from a standardized “Diagnostic Form” completed for each subject, which notes primary comorbidities. I am conducting my analyses in SPSS version 26. This research would shed light on the complicated relationship between psychotic disorders and substance abuse, as well as identify differences or similarities in prevalence between traditional non-biologically organized diagnostic groups and biomarker-based biotypes. By understanding how substance abuse interacts with biological markers in psychotic disorders, we can work towards learning more about the relative impact of substance misused on these already complicated illnesses, opening the door to potentially improving outcomes for individuals with these disorders.

Indi Khera

Prof. Sarah Keedy, Psychiatry

College Research Fellow (Hoeft)

Biological & Health Sciences, Neuroscience

Global modernization and urbanization have led to an increase in the number of vehicles owned and used worldwide. Developing countries in Sub-Saharan Africa, Asia, and Latin America have seen a dramatic increase in population in the last 30 years and in the number of vehicles on the road, especially in urban areas. Yet, the total number of cars, motorcycles, and bicycles in these countries varies based on data source. Vehicle registration is often not enforced, especially for motorcycles, which creates major discrepancies between the number of working vehicles present in country and the reported vehicles. Countries such as the United States and most of Western Europe have widely utilized vehicle registration systems. Yet, there is often a discrepancy between these numbers and data collected from nationally represented surveys and censuses. In this study, we aimed to collect vehicle registration, census, and nationally representative survey data from every country to compare sources and predict the number of households that own a car, motorcycle, and/or bicycles. Our data suggest that these numbers are underestimated globally. We recommend that new survey and census methods should be implemented on a global scale to accurately count the number of vehicles on the road. Furthermore, this data should be used to develop road traffic policies in developing countries to prevent road injuries and deaths.

Jaeda Roberts

Prof. Kavi Bhalla, Public Health Sciences

College Research Fellow

Biological & Health Sciences, Environmental & Urban Studies, Public Policy

The effective management of aortic diseases, such as dissections and aneurysms, requires the assessment of diseased and non-pathologic (normal) aorta morphology. The current representation of aorta geometry in the literature includes linear measurements of maximum diameter, as well as centerline-based measurements of tortuosity. However, the complexity of aortic pathology warrants the examination of geometric features that go beyond such linearization. The characterization of normal aorta geometry will establish a baseline for comparison with surface curvature of fragile aortas and ultimately improve risk stratification in asymptomatic adults. We use tools from differential geometry to quantify variation in healthy thoracic aortas, specifically the Koenderink curvedness, an intrinsic measure of curvature, and shape index, a measure of local shape that is independent of scale. We studied a cohort of twenty-three trauma patients that presented to the University of Chicago Medicine without aortic pathology. We created models of each patient’s aorta based on their initial computed tomography (CT) scans and subsequent scans. Curvature calculation is performed on the entire thoracic aorta and results confirmed that normal aortas adopt a largely cylindrical geometry with a shape index distribution centered around 0.5. Unlike shape index which remained stable over time, curvedness varied between patients and within patients during one hospitalization. This indicates proportional size changes in the aorta, specifically the arch region. We found that the shape of an aorta can change substantially in a short period of time, which should be taken into account when planning various endovascular interventions. Our next steps are to build a large data set of normal aortic geometries in order to identify deviation in aortic geometry that puts patients at high risk for developing vascular disease and relate variation in aortic surface curvature to clinically measured parameters such as blood pressure and volume status.

Karen Yuan

Prof. Luka Pocivavsek, Surgery; Dr. Kathleen Cao, Surgery

College Research Fellow

Biological & Health Sciences

In the US, immigrants are disproportionately represented among overeducated workers in the labor market, relative to other workers in the same occupations. While prior studies have explored how overeducation (also referred to as overmatch) among immigrant workers shapes their economic and social incorporation in the US, few have investigated its relationship to physical health. Downward occupational mobility, such as overeducation/overmatch, however, has the potential to exact a toll on immigrant health through various stress mechanisms. For this project, we use the 2010 and 2012 waves of the Health and Retirement Study (HRS) to interrogate how education-labor mismatch shapes health outcomes among a representative sample of US and foreign-born older adults. Leveraging labor history as well as enhanced health and biomarker data collected in the HRS, we capture workers’ health and their experiences of education-labor mismatch. After applying sampling weights to account for the complex design of the HRS, we used descriptive and bivariate statistics to better characterize the distribution of mismatch and other characteristics in our sample. Then, we utilized linear and logistic regression models to assess the relationship between mismatch and health, controlling for specific covariates. Overall, we find overmatch to be positively associated with several deleterious health outcomes, including poorer self-rated health, smoking, and stress-sensitive biomarkers such as C-reactive protein and A1c. Further, the relationship between mismatch and health outcomes is stronger for immigrants compared to US-born workers. Our analysis offers a novel contribution to the literature by exploring how a unique manifestation of social inequality in the US, education-labor mismatch, may be especially consequential for the health and wellbeing of immigrants.

Laura Chen

Prof. Aresha Martinez-Cardoso, Public Health Sciences

College Global Health Scholar

Biological & Health Sciences

Analyzing the functional relationships between groups of neurons can help in understanding the dynamics and information processing of the brain. Prior analysis of mouse brain slices has shown that the neuronal triplets with the highest amount of synergistic information have high amounts of recurrent connections, while those with the lowest amount of synergistic information have high amounts of feedback connections. However, it is unclear if the same pattern holds in vivo. To analyze this, I used various spike trains that were inferred from calcium fluorescence traces of V1 in a mouse viewing drifting gratings, and calculated the pairwise and joint transfer entropy for all pairs and triplets of neurons in each dataset. Next, I used the pairwise transfer entropy as an adjacency matrix for a functional network of neurons. In order to see if connection strength impacted the results, I thresholded the transfer entropy matrix at various percentiles between 10 and 99.5, and only counted values above the threshold percentile as connections. After constructing these networks, I categorized all the triplets in each network by their motif and graphed the distribution of the synergy values for each motif. However, in contrast to the previous work, high synergy was positively correlated with the number of feedback connections in a triplet. This pattern held across all the datasets and all the thresholds, and was most prominently present in networks with more neurons. Additionally, when the synergy values were normalized by the entropy of the target neuron, high synergy values were still positively correlated with the number of feedback connections. Therefore, in vivo and in vitro triplet motifs show opposite structural correlations with synergy, suggesting that there exist major differences between the functional relationships between neurons in living brain tissue and organotypic slice culture.

Leya Luo

Prof. Jason MacLean, Neurobiology, Grossman Institute

Dean's Fund for Undergraduate Research Awardee

Neuroscience

Nosocomial infections due to Staphylococcus aureus pose a significant problem in healthcare today, particularly with the rise of methicillin resistant strains. Protein secretion plays an important role in the pathogenesis of S. aureus infections. Recently, the type VII secretion system (T7SS) has been found to be required for virulence of S. aureus in the mouse model. The T7SS assembles in the bacterial membrane and promotes secretion of proteins with WXG-motifs and other effectors like the nuclease EssD. Secretion of these substrates relies on the peptidoglycan hydrolase EssH. The CHAP domain in EssH confers hydrolytic activity, however the rest of the protein’s function has not been elucidated yet. To date, the mechanism by which EssH promotes secretion through T7SS is not known. This research aims to investigate how EssH interacts with T7SS and how it promotes the secretion of its effectors. We hypothesize that peptidoglycan hydrolysis might be necessary either for T7SS assembly in the cell envelope or to facilitate substrate passage through the peptidoglycan layer. Previous work suggests that EssH interacts with the T7SS machinery, however the interacting surface of EssH is unknown. To test whether the EssH domain of unknown function (DUF) is responsible for this, we generated S. aureus deleted for DUF and tested whether this variant co-purifies with the T7SS machinery. In addition, we probed assembly of the T7SS machine in the cell envelope of the DUF mutant. Finally, we investigated whether T7SS-secreted proteins get trapped in the peptidoglycan layer of the DUF mutant. The EssH protein provides a unique area of study as it does not induce lysis of staphylococci despite exhibiting peptidoglycan hydrolase activities. Since EssH is required for protein secretion via T7SS, understanding more about its function on a molecular level presents a crucial opportunity to develop methods dedicated to decreasing S. aureus pathogenicity.

Maria Krunic

Prof. Dominique Missiakas, Microbiology; Dr. Maksym Bobrovskyy, Missiakas Lab

Biological & Health Sciences

The Wnt-signaling pathway is evolutionarily conserved due to its fundamental role in embryonic development, cell proliferation, and differentiation. In the absence of Wnt ligands, ß-catenin is degraded in the cytoplasm, however when Wnt signaling is active, the degradation process is interrupted, and ß-catenin enters the nucleus. As ß-catenin accumulates in the nucleus, it binds the transcription factor TCF7 and activates Wnt regulated genes. TCF7 collaborates with multiple other transcription factors to effect thymocyte development including HEB. Dysregulation of the Wnt pathway results in overexpression of ß-catenin which can lead to leukemogenesis, which is commonly observed in human T-cell Acute Lymphoblastic Leukemia (TALL). Stabilization of ß-catenin in developing T cells stalls their development at the CD4+CD8+ (double positive or DP) stage (CAT mouse model). The affected DP T cells are genomically unstable and predisposed to leukemogenesis. It was observed that when TCF-7 was knocked out from T cells with simultaneous ß-catenin stabilization (CAT-TCF), the leukemia did not develop, however T cell development was still blocked. In contrast, the potential cooperation of HEB with ß-catenin in thymocyte development and leukemogenesis is unknown. Early observations indicate that HEB knock out mice with ß-catenin overexpression (CAT-HEB) develop lymphomas that are molecularly distinct from the aberrant ß-catenin lymphomas, while the development of T cells is restored. Through ATACseq and RNAseq analysis, we have found that these CAT-HEB lymphomas may be driven in part by dysregulation of several ribosomal proteins and metabolic pathways through a dramatic increase of TCF7 binding sites. Through continued research, we hope to better understand the Wnt signaling pathway as well as the activities of stabilized ß-catenin with its partner transcription factors. If we are able to better understand the cooperation of ß-catenin with HEB and TCF7 and the mechanisms involved, our work may provide information for future treatment strategies for TALL.

Melissa Tracy

Prof. Fotini Gounari, Immunology; Stephen Arnovitz, Gounari Lab

College Research Fellow (Hoeft)

Biological & Health Sciences

Low-complexity regions (LCRs) are important for modulating the formation of many biomolecular condensates, but the sequence-function relationship of LCRs remains unclear. Finding evolutionarily conserved sequence features in related LCRs would inform searches for function. However, many LCRs are largely unalignable, hindering analysis through conventional alignment-based evolutionary approaches. To address this fundamental challenge, here we model the sequences of LCRs using the joint probability distributions of sequence features, which circumvent the need for residue-level homology in sequence comparisons, thereby permitting alignment-free evolutionary analysis. By targeting poly(A)-binding proteins (PABP), a canonical stress-granule marker whose LCR modulates its condensation, we demonstrate that the analyses routinely carried out on aligned sequences can be satisfactorily performed on unalignable LCRs using our model. Importantly, the Jensen-Shannon distances between sequence-based probability distributions can estimate the phylogenetic distances between PABP LCRs and this estimation is comparable to that achieved by quantifying sequence similarity between PABP structured domains using alignment-based methods. Moreover, we show that our model captures the majority of the sequence information in PABP LCRs and can be used to identify evolutionarily conserved sequence features despite poor residue-level conservation. Our future work will focus on broadly applying our promising new approach to other unalignable protein regions.

Rosalind Pan

Prof. D. Allan Drummond, Biochemistry and Molecular Biology

Liew Family Research Fellow

Biological & Health Sciences

On March 12, 2020, the cast and crew of Court Theatre’s production of "The Lady from the Sea" gathered for the last time to discuss closing in response to the COVID-19 pandemic hours before their first preview. As theatres shut down across the city that day, one question arose: how would the pandemic impact American theatre as we know it? In response, Dr. Eric Colleary of the Harry Ransom Center at UT Austin created the Theatre 2020 project, which aims to preserve a digital archival record of the impacts of the events of 2020 on theatres nationwide. In my research, a subcomponent of this project, I investigate one case study: Court Theatre. Court’s simultaneous connections with the University of Chicago, the South Side, and the broader Chicago theatrical community place it at a unique intersection of perspectives and communities unlike that inhabited by any other American theatre, making its response to both the pandemic and the Black Lives Matter movement particularly significant. By collecting various documentation of the past year, including but not limited to production documents, online performance recordings, photographs, interviews with staff, antiracism vision documents, podcast recordings, and more, I explore an unprecedented year in the life of an American theatre. Court’s work in both continuing to make art in a pandemic that left thousands of theatre workers unemployed and actively changing its practices to become an antiracist institution reveal a creative, intentional response to the multifaceted pressures of a year unlike any other in the history of American theatre.

Gabriela Garcia

Ms. Nora Titone, Court Theatre, Dr. Eric Colleary, Harry Ransom Center

CRASSH Scholar

History, Visual & Performing Arts

Even is a Tungusic Language spoken by a minority ethnic group within Russia known as the Even, Oroch or Lamut. With no more than 4,500 speakers, the documentation and understanding of this language is an invaluable pursuit. Like other Tungusic languages, Even has a complex case system with a theorized 13 cases. Of these cases, eight are semantic cases that express a variety of temporal and spatial relations. Additionally, Even has been attested to have a river-based orientation system which mirrors similar systems found in other Tungusic languages such as Evenki. The purpose of this initial study is twofold. First, I wish to assess the use of these semantic cases. Using recent data gathered by Professor Lenore Grenoble in 2019 and previous work done on Even, I attempt to determine the contemporary uses of these cases to describe space. Second, I evaluate existing experimental techniques and literature on spatial orientation systems with particular attention on work dedicated to describing river-based systems. After which I propose experimental methods for future work on Even in regard to this area. While just an initial study of these relationships, I hope that it can help draw implications for how space is created within the Even language and possible routes for future inquiry.

Jonathan Wuwong

Prof. Lenore Grenoble, Linguistics

Linguistics

Language is a central component of the human experience. When we communicate, listeners use acoustic cues to categorize sounds into discrete phonemes. For example, duration and formant frequency are two cues used to distinguish the vowel /i/ in “sleep” and the vowel /I/ in “slip”. Individual variation has been demonstrated in cue weighting such that some speakers may prioritize one cue more heavily than other speakers, yet relatively little is known about the mechanisms underlying these differences. We hypothesize that speech production impacts perceptual cue weighting. Two phoneme contrasts are studied in this project: /b/ and /p/ as in “back” and “pack”. The cues distinguishing /b/ and /p/ are voice onset time and fundamental frequency. Perceptual cue weighting between these cues was measured via an eye tracking paradigm in which subjects heard a word containing either /b/ or /p/ and clicked on the picture corresponding to the word among a group of pictures. By tracking their eye movement and timing where their eyes move to as they hear the cues in the acoustic signal, we can study their relative weighting of cues. Production data were obtained when subjects read sentences to the pace of a metronome and stories containing words with the relevant contrasts. The data collection process ended in March 2020. The production data are currently being processed via forced-alignment in WebMAUS and manual alignment in Praat. Mathematical values for the degree of cue weighting and values for the cue variation in the production data will be calculated in R. If values from the perception data are correlated with values from the production data, it will indicate that individual variation in speech perception impacts individual variation in cue weighting.

Nicholas Aoki; HenryMackall

Prof. Alan C. L. Yu, Linguistics, Phonology Lab

College Summer Research Fellow, CRASSH Scholar, Dean's Fund for Undergraduate Research Awardee, Liew Family Research Fellow

Linguistics

Incredible amounts of queer ephemera, histories, and memories have found permanent residence in archives like the Queer Zine Archive Project, among others. There are also instances and representations of queer experience that are nestled in other archives that do not have specifically queer intention, that suffer from how the traditional archival method of passive accumulation tends to reproduce knowledge-power structures, thus ostracizing marginalized stories from a place of prominence in the archive. These queer items, in various archives, might be inadequately represented by the metadata framework or dulled by its presentation. This thesis project aims to analyze this problem and its attempted solutions and suggest an additional way to present queer material from the archive. At the heart of this suggestion is Twine, created in 2009 by Chris Klimas as a software for creating works of interactive fiction. Twine has since been used to create countless works that prove its ability to highlight temporality, expose the implications of power, and emphasize the experience of navigation and exploration that is emblematic of archival excursion. As a platform that gives important space and tools to queer writers and game designers, it can give a new voice to the items that reside in archives, by animating, energizing, and connecting documents and writing that usually reside statically and boxed-in within the archives themselves. Aspects of Twine will benefit the material it encounters, without disregarding the archival process, and speak to a specific mode of presenting archival material. This project will be part praxis: I will present archives and their materials through the medium of Twine in order to lift up what has been flattened by the archival process and give attention to the queer lives these objects once lived.

Nicholas Peno

Prof. Ellen MacKay, English Language and Literature

Gender and Sexuality Studies, Humanities

I am conducting a technical art historical study of "Socrates Tearing Away Alcibiades" by Jean Baptiste Regnault. Regnault’s work can be situated in the context of the French Neoclassical art historical period. A visual of the initial underdrawing of "Socrates Tearing Away Alcibiades" may reveal crucial choices made by the artist. In order to accomplish this goal, I will conduct IR photography, which makes use of longer wavelengths of light which can ‘pass’ through the surface of a painting to enable aspects of the underdrawing to be reflected back into a specially modified camera. The camera lens will be covered with a series of external filters so that noise (color) from the visible spectrum is gradually reduced. Generating such images would help explicate the nuances of Neoclassical perspective(s) missed by historians who attempt to paint the period with all too broad of a stroke. Furthermore, this research may help explain subtle differences between this painting and its sister of the same name at the Louvre.

Talia Ratnavale

Dr. Issa Lampe, Smart Museum of Art Feitler Center; Dr. Lisa Zaher, School of the Art Institute of Chicago

Smart Scholar

Chemistry, History, Visual & Performing Arts

Our project aims to establish the existence of a lexicon of meaningful gestures whose interpretation is stable across individuals and to assess the demographic factors that influence familiarity with various gestures. Much research has been done on the use of co-speech gestures. Unlike the type of movements that are usually thought of as gesticulation (which includes gestures of emphasis), the gestures that we are studying have specific and fairly arbitrary codified meanings. Gestures of this kind are referred to in gesture research as “emblems”. In order to study these gestures, we are building a 1,000 unit catalog of animated GIFs (short, looping, silent video clips), which currently contains 576 files. Each of these GIFs contains an emblematic gesture coding distinct linguistic information. Electronic, text-based communication platforms, such as iMessage, Facebook Messenger, and Slack, allow the use of these GIFs, and the fact that such clips are widely available gives us preliminary validation that the gestures contained within them communicate consistently interpretable meanings. Our project focuses on the creation and dissemination of electronic multiple-choice surveys using SurveyMonkey and Mechanical Turk in order to identify gestures with consistently shared interpretations. Our anonymous surveys are accompanied by short, optional demographic questionnaires. By collecting large amounts of survey data, we will be able to identify which social groups share meanings for certain gestures and identify a subset of gestures that make up a broadly shared gestural lexicon.

Wren McMillan

Prof. Jason Riggle, Linguistics, Chicago Language Modeling Lab

College Research Fellow (Hoeft)

Humanities, Social and Behavioral Sciences, Linguistics

The present work proceeds by offering an interpretive reconstruction of Gottlob Frege’s theory of Sense and Reference, highlighting the problem of empty references, motivating Frege’s solution thereto, and offering an original two-pronged argument in opposition to it. Through its argument, the work decisively demonstrates that the ideal scientific language Frege prescribes is in fact unfit for science since it takes away the imaginative power demonstrated to be inherent to it and ignores the notion that meaning generation and thereby truth discovery stems from an interplay of senses rather than of references. Frege’s potential counterarguments appealing to his notions of indirect speech and mock thoughts are duly considered and refuted for producing more ambiguity and inconsistency than clarity. Above all, the research encourages further examination of the great founder of modern philosophy of language.

Kyle Shishkin

Prof. Benjamin Callard, Philosophy

Dean's Fund for Undergraduate Research Awardee

Philosophy of Language & Philosophy of Science

Modern physics research has identified artificial intelligence (AI) as a powerful tool for solving complex problems; one should ask, however, if such tools can lead to a deeper understanding of these problems, or equivalently if humans can learn from the solutions. To answer this question, we consider a simple pursuit-evasion game, “Cat and Rat”, where the “Cat” attempts to catch the “Rat” and the "Rat" attempts to escape. Based on simple physical laws, we construct a 2D simulator and employ the known effective guidance law of Augmented Proportional Navigation (APN) as the baseline strategy for the Cat. We then apply a Cartesian Genetic Programming (CGP) AI algorithm to control the Rat to attempt escape. We show that CGP was consistently able to counteract APN for a wide range of parameters. More importantly, we note that CGP offers human-readable solution output. To this end, we demonstrate how the CGP output allows us to realize a new Rat strategy and to improve our performance in counteracting APN. We argue that this ability to learn from AI is a primary benefit of CGP and that this learning is critical to the use of AI in physics.

Callum Welsh

Prof. Cheng Chin, Physics, James Franck Institute, Enrico Fermi Institute; Connor Fieweger, Chin Lab

Physics

This project presents an X-ray study of the supernova remnant (SNR) population within our Galaxy and the Magellanic clouds (LMC and SMC). A more accurate data set exists for the latter due to better distance determination, while Galactic SNR properties have larger error bars due to uncertainties in distances. We study the relationship between the X-ray luminosity and remnant radius, limiting our sample to remnants for which reasonably well-defined measurements of total X-ray luminosity and size exist. We examine various trends in the data, taking into account estimated age and ambient densities given in the literature. We demonstrate how the X-ray luminosity to size relationship can sometimes help to constrain distance estimates, or reduce the error bars on derived properties. We assess the difference between the Galactic and LMC SNR distribution and find it can be explained by densities in the LMC being on average 30% that in the Galaxy. This agrees with the densities around X-ray SNRs in each galaxy. Our results show agreement between observed X-ray luminosities and predictions using a Sedov-Taylor solution. They offer a framework that may allow for convenient estimation of the evolutionary state and physical properties.

Chris Albert

Prof. Vikram Dwarkadas, Astronomy and Astrophysics

Astronomy and Astrophysics

Electrocatalytic CO2 reduction shows potential for conversion of CO2 to industrially useful chemical compounds, such as alcohols, carbon monoxide, and alkenes. However, the field has focused on aqueous media for these reactions, limiting high Faradaic efficiency to desired products due to a competing hydrogen evolution reaction (HER). Research on this reaction in organic solvents is in its early stages and may eliminate the competing HER. By investigating the solvation mechanics of this reaction in organic media, a more efficient reaction may become possible, as indicated by previous work showing that a minimally solvated cation may lead to desirable intermediates for this reaction. Nuclear magnetic resonance (NMR) was used to investigate solvation environment of the electrolytes in a nonaqueous medium. These results were compared to cyclic voltammetry (CV) and double layer capacitance (Cdl) values for the CO2RR against metallic Au and Cu as working electrodes. The CO2RR electrochemical performance was also correlated with intrinsic properties of each electrolyte solution, such as conductivity, solvent Gutmann donor and acceptor numbers, and cation alkyl chain length. The resulting NMR data analysis showed minimal evidence of differing solvation of the electrolyte cation regardless of the anion present, which shows that properties of the electrolyte anion are not influential on the solvation environment in DMSO. Because of this lacking impact of the anion on solvation behavior and CO2RR electrochemical performance, the next step to investigating the optimal environment for the CO2 reduction reaction in organic media is comparing organic solvents. A preferential solvation environment may improve experimental data and product distribution without introducing competing HER. From there, the pathway will be opened to explore further electrochemical properties to move this technique toward industrial scale conversion of CO2 to societally beneficial products.

Christopher Birch

Prof. Chibueze Amanchukwu, Pritzker School of Molecular Engineering; Reginaldo Jose Gomes Neto, Amanchukwu Group

College Summer Research Fellow, Liew Family Research Fellow

Chemistry, Engineering

As part of the Phase-I upgrade for the ATLAS experiment at the Large Hadron Collider (LHC), a new custom electronic system called the Global Feature Extraction (gFEX) module is being developed and tested. The gFEX unit is a Level-1 trigger detector that uses jet algorithms to select for large-radius jets - essentially a collection of final state particles that comprise a single parent object - typical of particles such as top quarks, W/Z bosons, and the Higgs boson. Some of the key upgrades the gFEX unit provides is that it will considerably enhance the selectivity of the Level-1 ATLAS trigger and will be capable of processing the entire calorimeter (a specific type of detector found at ATLAS) on a single electronics board, all while allowing for local event-by-event pileup (noise) suppression. The ATLAS Phase-I upgrade is a complex and ongoing series of updates involving several new systems, including the gFEX unit, all of which must work together to ensure smooth functioning of the ATLAS experiment at the LHC. Thus, an important task is the documentation and internal communication of the most up-to-date technical design and details of the gFEX unit to the various teams working on the ATLAS Phase-I upgrade. Additionally, it is essential to publicize ATLAS-approved information on the gFEX project to a wider audience in the physics community. One way to accomplish this is through a central gFEX website that collects and presents the most relevant information for quick and easy reference. The content of the webpage will be pulled from numerous GitLab repositories, Twiki’s, and CERN’s version of a document control system called EDMS. Aspects of website coding will also be presented, and future work on the webpage, such as ease-of-updating, will be explored.

Daniel Paraizo

Prof. David Miller, Physics

Physics

The size and shape of an atom cloud and the distribution of atoms inside are some of the most important observables that we can access in a cold atom experiment. Images of the atom cloud are often the exclusive primary data from which such information can be extracted. One widely used imaging technique is absorption imaging, where a camera records the shadow cast by the atoms when a laser is shone into the camera through the atom cloud. However, several additional effects can complicate the imaging process and make one extract wrong atom numbers from the images. Under laser illumination, the atoms can accelerate and have their energy levels slightly shifted, leading to a misrepresentation of atom distribution on the image. Saturation effects might also cause the atom number recorded on an image to be lower than actual. Conventional imaging processing techniques does not retain the necessary information to account for such systematic errors in the atom numbers. In this research, we improve the imaging analysis procedure with the help of a more sophisticated analysis which, for instance, takes into account the saturation effects. This analysis procedure improves the quality of information extracted from the atom cloud in our Lithium-6 experiment. It might also be useful for a wider range of cold atom setups where different atomic elements are used.

Huiting Liu

Prof. Johannes Hecker Denschlag, Institute for Quantum Matter, Ulm University, Germany

College Summer Research Fellow

Physics

We propose a technique to use switchable fluorescent molecules to image localized energy depositions in a whole-body Positron Emission Tomography (PET) scanner. A gamma ray scatters multiple times in an organic solvent and generates Compton electrons. The electrons deposit energy in the organic solvent proportional to the energy of the scatter. The excitations transfer energy to initially non-fluorescent switching molecules and activate them into a fluorescent configuration. The activated molecules can be repeatedly excited by optical photons, yielding many fluorescence photons each before being reset to the inactive configuration. This technique would be applied to generate high-resolution images of gamma scattering events inside scintillator-filled modules arranged in a cylinder around the patient. The time of each Compton scatter is determined using prompt scintillation light detected by a photodetector with time resolution on the order of 50 ps. Selective illumination of the module from various angles would allow iterative refinement of the electron paths and then the detailed structure of the event. Combined with precise temporal resolution, the positron annihilation in the patient between opposing modules can be reconstructed to within a thin needle-like region of total volume on the order of 1 mm3. The number of activated molecules takes a role analogous to the light yield of a conventional scintillator, providing a measurement of the energy. The geometry and energies of the successive Compton scatters can be used to constrain and reject in-patient scattering background. There exists at least one class of well-studied molecules which may be capable of meeting the requirements of the technique.

Joao Shida

Prof. Henry Frisch, Physics, Enrico Fermi Institute

Dean's Fund for Undergraduate Research Awardee, Liew Family Research Fellow

Biological & Health Sciences, Chemistry, Engineering, Physics

We report on the completion of the new Exposure Time Calculator and graphical interface for MAROON-X. MAROON-X is a radial velocity spectrograph designed to detect Earth sized planets orbiting mid to late M dwarf stars. Now in regular operation at the Gemini North telescope in Hawaii, those who plan on using MAROON-X now have access to its new Exposure Time Calculator, a graphical interface designed to output useful information when collecting data with the instrument. By inputting a number of fields corresponding to the user’s observation conditions, such as exposure time, magnitude and spectral type, the Exposure Time Calculator will generate the predictive radial velocity measurement precision for the instrument. A fully interactive web-based tool, MAROON-X’s ETC provides real time updates to fit specific observation conditions, along with the functionality of allowing users to save all generated plots for later use.

Jorge Sanchez

Prof. Jacob Bean, Astronomy and Astrophysics; Prof. Andreas Seifahrt, Astronomy and Astrophysics

College Research Fellow (Hoeft)

Astronomy and Astrophysics

The creation of biocompatible nanoscale devices for biological modulation of cells and tissues possess the potential for tremendous impact on a variety of technologies, such as those in medicine. Typical medical devices and therapies tend to be microscale, comprised of non-biocompatible materials, and broadly targeted, resulting in imprecise treatments and adverse effects such as chronic immune response and tissue damage. The development of nano-enabled and biocompatible technologies – ranging from biodegradable nanoparticles for localized drug delivery to transient electronic devices for stimulation therapy to engineered biofilms with applications to nanomedicine – will continue to enable the advent of personalized medicine. This presentation discusses recent research into this frontier through synthesis and biocompatibility considerations before delving into latest advancements for cardiac, neural, and microbial modulation. Using these examples as a basis, future research directions in this field are described with an emphasis on explorations into biocompatibility for neural modulatory devices.

Kavita Parekh

Prof. Bozhi Tian, Chemistry

College Summer Research Fellow

Biological & Health Sciences

We study the dynamics of levitated particles under illumination by a laser. Microspheres ranging from 10 to 50 μm in diameter are levitated and trapped in a thermophoretic force field generated in a vacuum chamber with air pressures between 4 and 15 Torr. The laser heats up and creates a temperature differential in the levitated particles. Momentum exchange with the surrounding gas drives the illuminated particles either in the direction of laser propagation (positive photophoresis) or opposite the direction of laser propagation (negative photophoresis). We report observations of both positive and negative photophoretic forces on levitated particles. To understand our experimental results vis-à-vis existing models of photophoresis, we simulate the radiation field and temperature distribution in levitated spheres to to obtain quantitative predictions of the photophoretic and thermophoretic forces. This study of illumination-induced dynamics is a necessary first step towards optical control of levitated particles, which will find applications in studying micron-scale physics and force fields in a microgravity environment.

Kelsey Gilchrist; Huiting Liu

Prof. Cheng Chin, Physics

Physics

Much of what we know about the mechanics of solid materials can be ascertained by a surprisingly simple model: a collection of masses and Hookean springs. As one learns in first year physics, a Hookean spring exerts a tension in response to elongation or compression. Here, we ask how do the mechanics of solids change when the springs exert torques instead of tensions? In particular, it is known that geometric and topological properties of Hookean mass spring networks can predict features such as localized softness or rigidity. In this presentation, we will discuss how to generalize these ideas when the forces are transverse rather than longitudinal. Understanding the role of transverse forces in mechanical rigidity will shed light on the mechanical principles at play in complex media ranging from living organism to robotic materials.

Livia Guttieres

Prof. Vincenzo Vitelli, Physics (Topological Mechanics)

Dean's Fund for Undergraduate Research Awardee

Mathematics, Physics

My research concerns low surface-brightness galaxies (LSBGs). An LSBG is defined as a diffuse galaxy whose surface brightness is fainter than the ambient night sky by at least one magnitude. I specifically investigated LSBGs containing populations of objects that could potentially be globular clusters. My goal was to identify and analyze such LSBGs in the DES Year 3 data—theoretically, by measuring the luminosities of their globular cluster populations, we can calculate the distance to the host galaxies, allowing us to gain a better understanding of the cosmic distribution of LSBGs. From the DES Y3 LSBG data, I selected the largest LSBGs with the highest densities of objects masked by Source Extractor in their radius. This was a group of 68 galaxies. I then wanted to determine which of the objects around these galaxies were globular clusters, which was done by analyzing their properties and applying a cut based on their SPREAD_MODEL and MAG_AUTO values. I selected a group of nine LSBGs with the greatest number density of surrounding candidate globular clusters and hope to potentially submit a proposal for further imaging of these galaxies.

Louise Gagnon

Prof. Alex Drlica-Wagner, Astronomy and Astrophysics, Fermi National Accelerator Laboratory

College Research Fellow

Astronomy and Astrophysics

Laser cooling and imaging of neutral atoms rely on the absorption of photons whose frequency is in resonance with the atoms. The cooling efficiency and the imaging resolution are usually limited by the spectral purity of the light utilized to excite the atoms. Consequently, it is of great interest to develop narrow linewidth, ultra-stable laser sources in order to perform high fidelity experiments. In this poster, I will describe the construction of narrow linewidth 852 nm external cavity diode lasers (ECDLs) in the cat-eye configuration, which will be used for degenerate Raman-sideband cooling and fluorescence imaging of cesium atoms in the Quantum Matter Synthesizer experiment. I first discuss the cat-eye geometry and its advantages over other ECDL configurations due to an increased mechanical stability. I then consider different manners in which the cat-eye geometry can be implemented and present cat-eye lasers that were built. Their behavior is characterized and the influence of optical and electronic feedback on laser stability and linewidth is discussed. We observe a strong correlation between laser feedback and spectral linewidth and report narrow linewidths of less than 70 kHz and power outputs of up to 70 mW. Finally, we consider linewidth and output power limitations, how we can improve them and future experimental applications of the lasers.

Lucas Baralt Nazario; Connor Fieweger

Prof. Cheng Chin, Physics, James Franck Institute, Enrico Fermi Institute; Jonathan Trisnadi, Chin Lab, Jiamei Zhang, Chin Lab

Physics

The KOTO Experiment has collected 1.8 million events of neutral Kaon to three neutral Pion decay (denoted K_L→3π^0) over the course of recent data-taking runs which has yielded a large amount of π^0 decay data that is virtually background-free, offering a unique opportunity to study π^0 Dalitz decay. Neutral Pions typically decay through the electromagnetic force into two photons in (98.823 ±0.034) % of decays but can also undergo Dalitz decay where the Pion decays into a photon and an electron-positron pair. The branching ratio of this decay is calculable within quantum electrodynamics and has been measured to be (1.174 ±0.035) % which has an uncertainty of three percent of the value of the measurement. The KOTO π^0 decay dataset can be used to make a more precise measurement of the Dalitz branching ratio with an uncertainty of about one percent. The E14 KOTO detector provides an excellent means of identifying π^0 Dalitz decay with a 2576 crystal CsI calorimeter covered by a plastic scintillator charged particle detector. To measure the π^0 Dalitz Decay branching ratio I am studying decay events with six hits on the calorimeter and energy deposits on the charged particle detector and comparing them with a dataset of simulated K_L→3π^0 decay events created using Geant4.

Michael Farrington

Prof. Yau Wah, Physics, Enrico Fermi Institute

College Research Fellow

Physics

Supersymmetry, the symmetry between bosons and fermions, plays an essential role in our modern understanding of the universe. It is usually desirable to formulate a supersymmetric theory in the superspace formalism because the symmetry generators can be represented as “geometric symmetries” of superspace. However, models with extended supersymmetry, which attract much attention in the study of string theory, require additional constraints on superspace. By deriving the required constraints on the Lagrangian couplings, we develop a superspace formulation of quantum mechanical gauge theory with sixteen supersymmetries.

Sam Li

Prof. Savdeep S. Sethi, Physics, Enrico Fermi Institute, Kadanoff Center for Theoretical Physics

College Research Fellow

Physics

The preparation of sturdy, effective anti-icing surfaces is important in many industries such as aviation. Ice formation on aircraft wings, for instance, can cause a 25% increase in drag and 90% reduction in lift, while ice accretion on wind turbines can decrease annual energy production by 17%. Despite this pressing technological need, there is limited understanding behind the nucleation processes of ice on surfaces. Recent computational studies suggested that the soft confinement of water into nanoscale domains enables liquid water to exist at the surface well below freezing temperatures, significantly reducing any ice adhesion. My goal is to experimentally probe this further though the use of hygroscopic polymer coatings. Specifically, I plan to understand how soft confinement impacts ice nucleation and growth and to develop novel experimental techniques to probe the buried polymer-ice interface. First, I’ve been focusing on creating different polymer surfaces with long range order through the application of Directed Self-Assembly (DSA), a physical phenomenon in which block-copolymers tend to self-organize into ordered arrays of monomers when annealed onto a surface. Herein, we propose the utilization of DSA by annealing and etching standing cylinder-phase Poly(styrene-b-methyl methacrylate) to create a surface with specifically tailored anti-icing properties. My initial results demonstrate the success of etching with ultraviolet radiation to create an ordered nanoporous surface. Utilizing an advanced cooling stage with humidity control, my goal is to then measure the effects of soft polymer confinement by calculating surface free energy and adhesive force constants. Understanding the role of soft confinement on the heterogeneous catalysis of ice formation will help elucidate how to properly control ice growth and adhesion at the nanoscale and ultimately, when combined with our collaborator’s simulations, will lead to a dramatically improved understanding of how roughness and liquidity at interfaces impacts ice adhesion and detachment.

Wilson Turner

Prof. Steven J. Sibener, Chemistry, James Franck Institute

Liew Family Research Fellow

Chemistry

Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a rich group of natural products with great therapeutic potentials. Post-translational modifications (PTMs) endow RiPPs with structural rigidity and resistance to cellular degradation, and the PTM enzymes are often promiscuous so that it is possible to diversify the substrate peptide without threatening the PTMs. Because RiPPs are genetically encoded, library construction and screening can be carried out in a high-throughput fashion. Based on these features, we envisioned a method for drug discovery that includes the construction of a diverse library of randomized RiPPs and a competent selection platform to screen for properties of therapeutic relevance, such as protein binding and protein-protein interaction inhibition. Using ProcA2.8 and its variant XY3-3, we have tested two bacterial two-hybrid systems as selection platforms. While ProcA2.8 does not interact with the UEV domain of human Tsg101 protein, XY3-3 binds to UEV and inhibits the p6-UEV protein-protein interaction. By quantitatively characterizing ProcA2.8 and XY3-3 for inhibiting the p6 and UEV interaction, we were able to evaluate the fitness of these platforms for selections of protein binders or protein-protein interaction inhibitors. We chose the platform with a luminescence readout for our following selections. In the future, we will modify and optimize the platform to screen for highly functionalized peptides with therapeutic benefits. In particular, the latest genome mining efforts of the metagenomes of the human gut microbiota have provided us a great amount of novel RiPPs that have the potential to be adapted for library construction and screening. The screening process provides invaluable insights into the enormous potential of RiPPs in drug discoveries.

Yuhan Xu

Prof. Weixin Tang, Chemistry

College Summer Research Fellow

Biological & Health Sciences, Chemistry

In observational astronomy, weather, satellites, high-energy particles, and noise of various kinds obscure the primary signal of interest. Large-scale astronomical surveys are growing in size, precision, and complexity, which will incur more information in images, and this information includes more potential sources of noise. Conventional algorithmic tools for image de-noising are challenged to handle efficiently the huge workload of the task of image reduction Therefore, developing automated tools such as convolutional neural networks (CNN) for denoising has become one of the most promising methods. However, current supervised learning algorithms require prior knowledge of the morphology of the target objects, which significantly limits the applicability of denoising neural networks. Our research project utilizes a self-supervised algorithm, which does not require any prior knowledge of the signal, to develop a framework for denoising astronomical images. We performed experiments on our self-supervised algorithm with several neural network architecture of different variety and complexity, testing our overall framework with simulated noisy images of different noise realization. We examined our results by comparing them with the pristine ground-truth (noiseless) images. In our experiments, despite insufficient accuracy in recovering the amplitude of the object signal, our algorithm demonstrates satisfying capability in recovering morphological characteristics of the simulated objects. We conclude that our self-supervised algorithm may only have limited application in the signal modeling for catalogs of large astronomical surveys. However, it may contribute to tasks that involve processing astronomical images with complicated morphologies such as the search for gravitational lensing.

Yunchong Zhang

Dr. Brian Nord, Astronomy and Astrophysics, Fermi National Accelerator Laboratory

College Summer Research Fellow

Astronomy and Astrophysics

Amorphous carbon (a-C) is a common form of carbon material with broad ranging applications in industry. Computer simulations of a-C enable a theoretical investigation of its structural and electronic properties. One such property is the energy difference between the highest occupied molecular orbital and the lowest unoccupied molecular orbital. This difference determines the minimum energy required for an electronic excitation, and it is modulated by electron interactions with the lattice at finite temperatures. This modulation is referred to as the band gap renormalization. Accurate determination of the band gap renormalization in the low-temperature quantum regime requires computationally expensive path-integral molecular dynamics methods to fully address the effects of nuclear quantum motion. The high structural disorder of a-C gives rise to different amounts of band gap renormalization depending on the chosen sample. Distinct structural signatures of such samples motivate the search for suitable descriptors of the band gap renormalization, which can be used, both to predict the renormalization without the need for expensive simulations, and to offer a new window into probing the renormalization experimentally. In this work, we determine the zero-point band gap renormalizations of seven a-C samples at 3.25g\/cm^3 using molecular dynamics with quantum thermostat where forces are obtained by solving Kohn-Sham equations within generalized gradient approximations. We then correlate structural properties with the band gap renormalizations, forming the basis for constructing predictive models. The construction of such models will allow for the efficient computational and experimental determination of the zero-point band gap renormalization in a-C, important for the development of a-C based semi-conductor devices of the future.

Yunxiang Song

Prof. Giulia Galli, Pritzker School of Molecular Engineering; Dr. Arpan Kundu, Pritzker School of Molecular Engineering

Liew Family Research Fellow

Chemistry, Physics

Following the murders of George Floyd and Breonna Taylor this past summer and subsequent protests, there have been increasing calls to scrutinize and reform policing methods in cities across the United States. Many cities of varying sizes, complying with an Obama administration directive, have released detailed accounts of how police officers use their time to respond to citizen complaints (herein referred to as “Police Calls for Service Data”). As calls for transparency and reform continue to grow, this data will serve as a unique and insightful lens into current police practices in cities large and small across the United States. I have obtained Police Calls for Service Data from approximately 20 cities across the United States from public records. The data, obtained for the year 2019, range from about 7000 to nearly 2 million individual observations. I am using this wealth of publicly available Police Calls for Service Data to identify how police departments in cities across America respond to citizen complaints, the types of incidents they tend to spend their time responding to, and the degree to which some neighborhoods are policed and others are not. By generalizing these incidents into categories comparable across cities, analyzing individual incidents against their geography (down to the Census tract level), and collecting detailed information on when and for how long the police spend responding to incidents, I believe we can develop insights into how the police across multiple cities spend their time. Among other things, this analysis could shed light on inequalities in policing practices, both within and between cities, differences in how neighborhoods are policed, and the relationship between the characteristics of community demand and how the police spend their time.

Andrew Hallowell

Prof. John Brehm, Political Science

CRASSH Scholar

Law and Legal Studies, Political Science, Public Policy

Studies have shown that family conflict is correlated with adverse mental health outcomes among youth. The COVID-19 pandemic has led to new work patterns and family dynamics that have increased household tensions among families worldwide. Among Asian Americans, family conflict may be further impacted by the acculturation gap between immigrant parents and their U.S. born children, as well as increases in racism against Asian Americans. The confluence of these sociocultural stressors during a pandemic places significant burden on Asian American families, likely affecting their mental health. This study will examine the association between increased family conflict and young adult mental health outcomes during the COVID-19 pandemic in a sample of 70 Chinese American young adults. We hypothesize that during the COVID-19 pandemic increased family conflict will be associated with poorer mental health, specifically higher levels of anxiety and depression. This study sampled 70 Chinese American young adults between the ages of 18 to 25. Each participant completed an online survey that assessed dimensions of stress response, mental health, and family conflict in addition to other measures. 30 participants were then selected from the broader survey sample to participate in one-hour semi-structured interviews which sought to elucidate the unique pressures and responsibilities incurred upon families during the COVID-19 pandemic. The findings of the study will seek to reveal links between family conflict and mental health outcomes during the COVID-19 pandemic, and illuminate the mechanisms by which this interaction occurs. Given that family conflict has been shown to be associated with adverse mental health outcomes, an understanding of the impact and nature of family conflict during the COVID-19 pandemic is important in helping to inform potential interventions seeking to improve mental health outcomes during and after the pandemic.

Bryan Gu

Prof. Miwa Yasu, Crown Family School of Social Work, Policy, and Practice, Cultural Mental Health Development Lab

Social and Behavioral Sciences

The STEM gap is one of the most glaring examples of gender inequality, and although gender differences in math attitudes have been identified as a possible cause of the gender STEM gap, there have been few studies that have decomposed gender into a more complex variable, instead imposing a binary gender construct in studies of math attitudes. The purpose of this study was to investigate the relation between gender identity and math attitudes, with an updated definition of gender as a spectrum rather than a binary. Adult participants (N=500) completed a survey with a combination of heavily validated measures of math anxiety, gender-math stereotype, trait anxiety, math self-concept, and gender, defining gender in a novel and complex way in order to understand if certain gendered identities, attributes, and experiences are correlated with math attitudes. By defining gender as a continuous variable on a spectrum as opposed to a binary and discrete variable through the combination of four measures of gender, notions of gender can be seen with more nuance. Preliminary results suggest that math anxiety varies on a spectrum rather than as a binary and ongoing research is expected to confirm that these results are reflected in the general population. Ultimately, the results of this study are the first to examine the math experiences of individuals who identify within non-binary gender in comparison to mainstream binary gender, and results elucidate how the STEM gap can be addressed not only with respect to women but also for those across the gender spectrum.

Emily Knopf

Prof. Susan Levine, Psychology

Gender and Sexuality Studies, Social and Behavioral Sciences

How do second generation immigrants perceive opportunity and community in ethnic enclaves? Using 26 interviews of second generation Latinx immigrants from the ethnic enclaves around the Chicagoland area, this paper seeks to understand how the assimilation process, specifically opportunities of socioeconomic advancement and a sense of belonging with the mainstream community, are perceived by second generation immigrants. Previous scholars have heavily theorized the trajectories of first-generation immigrants in terms of these conditions, suggesting that the assimilation into white, middle-class spaces is desirable. The following study seeks to interrogate these assumptions by looking at the experiences and perceptions of the second generation living in ethnic enclaves. I find that participants experience exclusion from the mainstream community through institutional and individual forms of surveillance, which undermines their sense of belonging with white, middle class communities. Participants find relief from this type of discrimination through cultural identification within their ethnic communities, which can become a catalyst for organizing and forming ethnic solidarity. Furthermore, I find that most participants define opportunity in terms of education and employment opportunities, which are severely lacking in their communities. There exists a tension in the way the participants view the assimilation processes, in the way they strongly identify with their ethnic heritage as opposed to white spaces, and the way they value opportunities for socioeconomic advancement even though the opportunities are not quite present in their own ethnic communities. These findings have implications in the trajectory of the second generation in ethnic communities, demonstrating the value of both cultural background and economic advancement.

Lisette Gonzalez-Flores

Prof. Robert Vargas, Sociology

Dean's Fund for Undergraduate Research Awardee

Comparative Race & Ethnic Studies, Sociology

Climate change presents many challenges for municipal planning across the nation. Changing weather patterns add new strain to infrastructure around the country. Pressure to develop infrastructure that is more resilient to climate change, have prompted some cities to announce the development of green infrastructure plans. One such plan is Chicago’s Green Alley Program, which started in the early 2000s. A green alley would serve as an auxiliary storm water management system, reducing storm water induced flooding by redirecting excess rain away from the MWRD sewer system. Green stormwater infrastructure throughout the country presents a new mode of sustainable urban infrastructure. One that integrates local ecosystems with built infrastructure in urban environments. Green alleys offer numerous co-benefits in line with the ecosystem services framework of environmental management. Little research has been done on Chicago’s green alley infrastructure. This paper quantifies the spatial distribution of Chicago’s green alleys and identifies spatial correlations with factors around the city which could affect the development of future sustainable infrastructure systems; factors such as patterns of rainfall and flooding, the distribution of existing green space, and socioeconomic indicators such as per capita income and building age. This paper also analyzes the implications of spatial correlations in terms of the broader history and context of infrastructure development across Chicago and what this means for the future of green infrastructure plans.

Javier Gaughan

Dr. Sabina Shaikh, Environmental and Urban Studies

Chicago Studies, Engineering, Environmental & Urban Studies, Public Policy

The 1971 Liberation War of Bangladesh saw the systematic employment of genocidal rape by West Pakistani forces against anywhere between 200,000 and 400,000 women. Post-independence, the left-liberal Awami League government venerated these women as ‘Birangona,’ or war heroines. Despite this public acknowledgement, the ‘Birangona’ label has invited great stigma and communal ostracization that persist to the present-day. Therefore, the public memory of Birangona women is a novel case study to examine the gendered memorialization of atrocity – whereas the predominantly male Bangladeshi soldiers from the War continue to be celebrated as martyrs and freedom fighters, Birangona women have been relegated to the sidelines of popular discourse about the 1971 Liberation War. To investigate this disparity, I turn to anthropological theories of gendered nation-building, as well as existing scholarship on the memorialization of atrocity. I will also draw from existing records of Birangona testimony to investigate the public afterlives of traumatic wartime violence in present-day Bangladesh, as felt by Birangona women themselves. Finally, I employ James Young’s formulation of the counter-monument (1992) to turn to alternate, dynamic ways of envisaging the public memory of Birangona women. I propose the formation of women’s circles around Bangladesh that center the lived experiences of Birangona women while also fostering horizontal and intergenerational bonds of solidarity among women in Bangladesh. Beyond redressing the gender gap of public memory about the 1971 War of Liberation, this research can hopefully address the immense difficulty that victims of sexual violence face worldwide in engaging with public memory in an equitable, trauma-informed manner. Moreover, these research findings may be a springboard to engage with the scant scholarship surrounding the memory of male survivors of wartime rape, both within Bangladesh and without.

Wahid Al Mamun

Dr. Amelia Klein, Crown Family School of Social Work, Family, and Practice

Anthropology

The Anatolian Atlas Project is a landscape archaeology project that utilizes remote sensing tools such as Geographic Information Systems (GIS), satellite imaging, and aerial photography in the Oriental Institute’s CAMEL Lab (Center for Ancient Middle Eastern Landscapes) to carry out integrated analyses of archaeological regions and sites that are often studied in very localized contexts. The benefit of using these remote sensing tools for archaeological research lies fundamentally in their potential to leverage survey information from diverse regional and temporal scales by drawing them into a single framework that can be used to assess overarching spatial trends. In its current stage, research on the Anatolian Atlas Project consists primarily of transforming information from archaeological publications into spatial data that can be manipulated through GIS technologies. This process requires several steps including: data entry, database construction, map making, historical referencing, and identifying archaeological sites from a remote perspective. So far, the Anatolian Atlas Project has led to the creation of unique spatial data for hundreds of archaeological sites and features across a research area covering most of present-day Turkey. The most tangible outcome of this research to date has been the creation of an extensive database that is accessible online and which allows for multiregional and temporal analyses to be carried out across the ancient Anatolian landscape. This research constitutes one of the first major attempts to make robust landscape data more widely accessible in the hopes that it can be used to raise a host of archaeological questions about the complex relationships of humans across the ancient landscape. Future work will consist of identifying more sites and integrating them into this growing database.

William Shine

Prof. James Osborne, Near Eastern Languages and Civilizations, CAMEL Lab, Oriental Institute

College Summer Research Fellow

Interdisciplinary Humanities, Social and Behavioral Sciences

The goal setting process can be separated into two phases: first, people deliberate which of their many goals to pursue and second, they plan how, when, and where to take action on their chosen goal. Because success in the first phase of this process entails choosing a goal that is feasible, individuals in this phase tend to become open-minded and realistic (a deliberative mindset). In the second phase, however, success entails taking action on one’s goal, which is why individuals in this phase tend to become focused and optimistic (an implemental mindset). While people naturally adopt both a deliberative and implemental mindset as temporary states when pursuing their goals, no research has assessed whether these mindsets can be characterized as stable personality traits. To test this hypothesis, we developed a self-report scale to assess how often people deliberate or plan in their everyday lives. If a deliberative mindset can be characterized as a personality trait, we expect people who frequently deliberate to be more open-minded and realistic than those who do not. Similarly, if an implemental mindset can be characterized as a personality trait, we expect people who frequently plan to be more focused and optimistic than others. Assuming the data supports these hypotheses, “deliberative” and “implemental” people might differ in ways other than how they set goals. It is not unreasonable to think that “implemental” people – who are optimistically planning the implementation of their goals – might be happier while “deliberative” people who weigh the pros and cons of their decisions might exhibit greater existential humility. This research could therefore reveal how the way we set goals shapes how we approach and interact with the world and people around us.

Zara Malik

Dr. Anne Henly, Psychology

Dean's Fund for Undergraduate Research Awardee

Social and Behavioral Sciences