A major technical limitation in the study of complex social behavior of freely moving rodents is the manual annotation of behavior because it is subjective, extremely time-intensive, and prone to observer drift. Simple Behavioral Analysis (SimBA) utilizes machine learning (ML) applications to automate behavioral analysis by using pose estimation to create supervised ML predictive classifiers of rodent social behavior. In a single project, thousands of videos need to be preprocessed, which includes locating individual trials, identifying behavioral events within each trial, and choosing trimming points to focus on specific outcomes or the presence of multiple animals. Manual editing amounts to thousands of hours, often yielding clips with inaccuracies in timing or content, and leads to inaccurate ML predictive classifiers. To address this problem, my research is centered around integrating behavioral metadata into a tool that can automate preprocessing steps with high precision to improve the quality of resulting classifiers. I attempt this via two major improvements. First, to eliminate the reliance on manual record-keeping, I will implement a function that utilizes metadata to link relevant time-stamped events to their corresponding behavioral experiment video. Second, I will leverage ML-based object detection, such as YOLO4, to determine time points when two animals are present, which often indicates that a social reward has been obtained. Through this project, when compared to manual scoring, I expect that: (1) there will be a significant cut in the time necessary to preprocess videos, (2) the yield of usable trials for SimBA will increase, and (3) that there will be an improved accuracy of pose estimation and classifier performance. Overall, these additions will greatly enhance the ease and flexibility of data preparation for highly specific behavioral analyses during the task, enhancing the efficiency of ML procedures to yield powerful behavioral classifiers.
 

The Neuropixels (NP) probe is a multielectrode array that can record from large populations of neurons with high temporal and spatial resolution, along a shank spanning multiple brain regions. Identifying specific neural populations recorded along the shank is critical for later determining their structural connectivity, adding further insight into their behavioral function. Due to the shank’s material, fluorescent dyes cannot be used for this purpose as the dye will disperse broadly. To solve this, we will use silk fibroin, a biocompatible molecule derived from the cocoon of Bombyx mori to encapsulate a fluorescent protein-encoding viral vector in a silk film that degrades after a controllable period of time. Viral approaches allow for genetic isolation of specific cell-types and circuits. We will combine herpes simplex virus with the silk film and apply it to discrete sections along the shank before insertion, to induce expression of green fluorescent protein (HSV-GFP) in nearby recorded neurons for visualization. First we will test a range of fibroin/HSV-GFP solutions to optimize targeted expression for acute recording applications. Following optimization, we will test the silk/HSV-GFP solution while recording from the mouse amygdala. Then, we will image the brain to visualize the neural populations that were recorded. We predict that the chosen silk/HSV-GFP solution will yield high expression of HSV-GFP in a localized region of the brain that corresponds to the coated subsection of the probe. In future experiments, we will combine the optimal solution with anterograde and retrograde viral tracers along the probes, allowing us to dissect the connectivity patterns of recorded neuronal populations. These experiments will integrate structure and function to derive greater insight from neurophysiological experiments during behavior in mice.

We recently introduced operant social stress (OSS), a new operant procedure that classifies social motivation in mice as they lever press for volitional social interactions with a familiar partner before, during, and after social stress exposure. For social stress exposures, male mice underwent social defeat and female mice underwent witness defeat. In social defeat procedures, mice are repeatedly exposed to physical antagonistic interactions by an aggressive, larger mouse, while mice exposed to witness defeat mice observe these interactions from across a perforated barrier. Consistent with the literature, male mice exposed to social defeat exhibited reduced social motivation, while female mice exposed to witness defeat displayed an increase in social motivation. These opposing observations suggest different underlying mechanisms, but it remains unclear whether lever pressing during the task truly represents a motivation for affiliative reward. Thus, to rule out the contribution of non-social factors impacting social self-administration, we performed two control experiments to rule out alternative interpretations in this new operant method. In Experiment 1, we removed the familiar partner from the waiting chamber, in turn removing the social aspect of the reward. In Experiment 2, we unpaired the social rewards from the contingent lever, instead randomly delivering them during each trial. We hypothesized, and observed, that these manipulations would prevent mice from acquiring operant responses in the task and rule out non-social factors in driving operant responding. With the inclusion of these control experiments, we can now directly assess the social motivation of both male and female mice, facilitating deeper investigations into the underlying mechanisms in future studies.

Justice-centered approaches to equitable computer science (CS) education frame CS learning as a means for advancing peace, antiracism, and social justice rather than war, empire, and corporations. However, most research in justice-centered approaches in CS education focus on K--12 learning environments. In this position paper, we review justice-centered approaches to CS education, problematize the lack of justice-centered approaches to CS in higher education in particular, and describe a justice-centered approach for undergraduate Data Structures and Algorithms. Our approach emphasizes three components: (1) ethics: critiques the sociopolitical values of data structure and algorithm design as well as the underlying logics of dominant computing culture; (2) identity: draws on culturally responsive-sustaining pedagogies to emphasize student identity as rooted in resistance to the dominant computing culture; and (3) political vision: ensures the rightful presence of political struggles by reauthoring rights to frame CS learning as a force for social justice. Through a case study of this \emph{Critical Comparative Data Structures and Algorithms} pedagogy, we argue that justice-centered approaches to higher CS education can help all computing students not only learn about the ethical implications of nominally technical concepts, but also develop greater respect for diverse epistemologies, cultures, and experiences surrounding computing that are essential to creating the socially-just worlds we need.

 The Hybiske Lab studies chlamydial infections in humans, and is currently working with a National Health and Nutrition Examination Survey (NHANES) set of serum samples from the Centers for Disease Control and Prevention (CDC) to determine the seropositivity rate of chlamydia in the U.S. by testing for the presence of anti- C. trachomatis [CT] antibodies in a large multidimensional collection of patient sera. The impact of this research is highly relevant today. Chlamydia was the most reported STI in the country in 2020 and one of the leading causes of Pelvic Inflammatory Disease (PID) in females. While prior research on the prevalence of chlamydia has largely focused on specific demographic groups, this study is one of the first to research its prevalence in the general and contemporary population across the country. Using patient survey data will also help us differentiate between rectal and genital CT infection. My work centers on a novel CT peptide-based enzyme-linked immunosorbent assay (ELISA) that achieves 93.9% sensitivity and 98% specificity, far outperforming other CT detection methods including commercial assays. An additional advantage of this particular assay is that it was designed with peptide-based specificity — using 24 unique peptides that are strong B cell antigens — for the species C. trachomatis, and thus does not suffer from cross-reactivity with the closely related respiratory pathogen C. pneumoniae. We have over 3000 patient sera samples to analyze using this approach, and the 96-well assay format allows for this large number of specimens to be processed at once. I have incorporated additional analyses in my workflow, like testing for the presence of immunoglobulin species specificity across this large sample collection. Based on the data from the small percentage of the total samples collected to date, we are working with a seroprevalence rate of over 20%.

Lacking in early emotional support has been associated with emotional dysregulation and impulsivity in adulthood. Although previous research has also demonstrated that emotion dysregulation and impulsivity are both crucial factors associated to alcohol-related problems, to our knowledge there is no study exploring the relationship between early emotional support and alcohol use in adulthood through the mechanisms of emotion dysregulation and urgency. Additionally, previous work has mostly relied on cross-sectional data. The current study aims to explore the association between early emotional support and alcohol use by assessing the role of emotion dysregulation and urgency as mediators. We use pilot data collected via cross-sectional and ecological momentary assessment (EMA) methodology. Emotion dysregulation will be assessed by the Cognitive Emotion Regulation Questionnaire (CERQ; Garnefski & Kraaij, 2001). Urgency was assessed by the averaged values of the negative and positive urgency subscales in the 59-item Impulsive Behavior Scale (UPPS-P; Whiteside & Lynam, 2001; Lynam, Smith, Whiteside, & Cyders, 2006). Early emotional support was assessed by the emotional support subscale in the Multidimensional Neglect Behavior Scale (Dubowitz et al., 2011). Alcohol use was assessed by the Daily Drinking Questionnaire (DDQ-R; Collins, Parks, & Marlatt, 1985). Longitudinal items were gathered from a subset of the above measures. For the purposes of this presentation, we plan to analyze the data using bivariate correlation analyses in preparation for a full mediation analysis in the full study. We expect to find that those lacking in emotional support during adolescence predicts both emotional dysregulation and urgency in adulthood, which leading to alcohol-related problems in adulthood. Results in the expected directions would suggest that low emotional support in adolescence may be a risk factor for substance abuse later in life, showcasing a need for caregivers to better the emotional states of their children.

 Cancer metastasis, the spread of tumor cells to different parts of the body, significantly increases patient mortality. An early step in the metastasis process is invasion into surrounding tissues. One way that tumor invasion is studied is through tumor organoids. Tumor organoids mimic tumors in vitro through 3D cell culture. While it is generally held that invasion continues to increase monotonically over time, I recently discovered that invasion of tumor organoids has a temporal pattern, where invasion spikes up, then decreases after a certain time. This finding suggests more complex regulation of invasion dynamics than thought previously. The goal of this project is to investigate the temporal dynamics of cell-matrix associated RNAs and proteins during breast tumor organoid invasion. I can perform a qPCR time course of particular genes related to invasion to measure the levels of RNA at specific time points. In addition, I can check for protein levels using a novel method developed in the Cheung lab. This method utilizes bio-orthogonal click-chemistry to perform rapid, selective pairing of intracellular proteins with azidohomoalanine, a clickable methionine analog. Click-chemistry allows us to pick up proteins that cells are either secreted or on the surface of the cells. To define a cancer-specific invasion signature of tumor invasion, I compare RNA and protein dynamics in breast tumor organoids with normal mammary organoids (FVB) migrating in 3D collagen gels. I hypothesize that there will be specific genes associated with increased and decreased invasion levels. In future work we will target those genes by either suppressing those genes that increase with invasion or increasing the expression of invasion suppressors. We expect this work to reveal new regulators of the metastatic process.