29th Denman Undergraduate Research Forum (2024)
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Item The Need to Feed: Differences in the Behavior of Black-Handed Spider Monkey (Ateles geoffroyi) Non-Lactating Females Versus a Lactating Female(2024-03) Lerner, Finn; McGraw, W. ScottPrimates have varying needs based on their life histories causing different members of the species to have different activity budgets. Lactating females require a higher nutritional intake to sustain lactation resulting in increased feeding. In the Osa Peninsula of Costa Rica, the activity budgets of three adult female black-handed spider monkeys (Ateles geoffroyi) were calculated to test the behavior of one lactating female (LF) and two non-lactating females (NLF). I hypothesized that LF will feed (feed, not moving and feed, moving) more than NLF to support lactation. A further prediction was that LF will spend less time with the other behaviors (rest; groom; and move, not feeding) than NLF. To record behavior, instantaneous focal sampling for three 10-minute sessions (one session per subject) was utilized with the behavior of one subject recorded at 30-second intervals for 10 continuous minutes. The following behaviors were evaluated: feed, not moving; feed, moving; rest; groom; and move, not feeding. The results found that the mean activity budget of NLF was: 65% rest; 25% move, not feeding; and 10% groom. Meanwhile, the activity budget for LF was: 30% rest; 40% move, not feeding; and 15% feed, not moving. For the remaining 15%, LF was out of sight and behavior could not be recorded. Thus, the first hypothesis is supported because LF fed more than NLF. However, the second prediction is partially supported because while LF groomed and rested less, LF moved more than NLF. The findings suggest that Ateles geoffroyi LF feed more to sustain lactation, but also move more which is likely due to foraging because of increased nutritional intake for lactation. Further studies would benefit from increased sample size, trial amount, and observational time since behaviors were only observed for 30 minutes with a limited number of individuals. Ultimately, the research demonstrates that members of the same sex within a species have varying behaviors, thus dividing their time differently based on needs, including maternal responsibilities.Item Crowd Scene Anomaly Detection in Online Videos(2024-03) Yang, Kaizhi; Yilmaz, AlperThe prevalence of surveillance cameras in public places has led to an extremely pressing need for effective position and crowd monitoring, as well as anomaly detection. This paper tends to exhibit an incorporated approach that combines state-of-the-art computer vision techniques for comprehensive crowd surveillance. The main features of our approach are summarized into four steps: (a) Object detection and tracking; (b) Geometric rectification for positioning; (c) Motion extraction; and (d) Anomaly detection. First, this uses YOLOv5's Convolutional Neural Network (CNN) model in making efficient detection of objects, focusing on spotting individuals within crowded scenes. After detection, a strong mechanism for tracking is established with the help of the DeepSORT algorithm, which can track the person across frames. It must gain the people's position in the video frame and analyze motion data with the guarantee of capture of camera-scene geometry. Each frame thus gets converted from the 3D perspective to a 2D bird's eye view within the surveillance video, giving a guarantee of capture of the geometry of a camera scene. Motion anomaly detection is addressed through statistical methods, with Kernel Density Estimation (KDE) being employed to identify deviations from normal motion patterns. Extensive experiments conducted on different online crowd scene video datasets validate the effectiveness of the proposed anomaly detection mechanism. Overall, this integrated approach proposes a promising solution to crowd surveillance, further development of object detection, tracking, and anomaly analysis for monitoring public spaces.Item Congressional Speech Networks: Their Formation and Importance(2024-03) Costanzo, Charles; Box-Steffensmeier, JanetCongressional speeches drive policymaking and political debate at the national level. As a crucial method of communication, these speeches directly reflect legislators’ political agendas and serve as a vehicle by which members of Congress can convey their political priorities and advocate for important issues. Prior to technological advances that made modern natural language processing methods computationally feasible, survey data and analysis of behavior in strategic settings (i.e. legislative roll-call voting) were used to analyze congress members' policy positions and social networks. However, both of these approaches lead to methodological conflicts; new surveys cannot capture past information and represent but a small snapshot of the present, while institutional rules constrain roll-call analysis. Congressional speeches, on the other hand, are less constrained by institutional rules and capture information over a period of time, thus providing a much deeper view into the positions, ideologies, and rhetorical relationships of members of Congress. Previous work applied well known natural language processing methods to determine the level of rhetorical similarity between speeches contained in the Congressional Record from 1981 to 2017, developing relational networks between members of Congress based on these similarities. These networks illuminated the lexical similarities between legislators, the links between rhetorical relationships, partisanship, and legislative effectiveness, and how rhetorical trends developed over three and a half decades. However, more work is needed to illuminate factors that contribute to the similarities in congressional speech that form the basis for network connections. This project extends previous work through the application of exponential random graph models to congressional speech networks, allowing for statistical analysis of the impact of various endogenous structural effects and exogenous covariates on the formation of congressional speech networks over time. Analyzing factors that contribute to the formation of network ties in each Congress provides significant insights into the evolution of relationships over time as well as the underlying dynamics and trends driving legislators’ rhetorical relationships. These insights improve our understanding of social ties in Congress and could even be used to inform strategies that aim to facilitate more effective political discourse and lawmaking in Congress.Item Effort: Unveiling the Dynamics of Laban's Qualities in Choreography through Comparative Analysis and Creative Exploration(2024-03) Federinko, Jack; Williams, Valarie; Perkins, CrystalThis research project examines the relationship between choreography and dance notator Rudolf Laban's theories of effort. To explore the significance of Laban's effort qualities in movement and choreography this project addresses the question: How do variations in notated qualities of space, weight, time, and flow impact the intention and emotion of choreography? This project explores these elements through interpreting/comparing dance notation scores of the same choreography, learning choreography, and exploring my choreographic and notation processes.Item Goodness-of-fit in Preschool-aged Children's Relationships with Mothers and Fathers(2024-03) Ni, Yinan; Schoppe-Sullivan, SarahThe concept of goodness-of-fit was initially proposed by Thomas and Chess in 1977, and pertains to the alignment between a child’s temperament and the requirements, anticipations, and possibilities present in their environment (Shiner et al., 2012). Goodness-of-fit is an important concept in understanding children’s development, especially in the preschool years, a critical period of development for children to refine their social, emotional, and behavioral skills (Trawick-Smith, 2014). In this study, we focused on three research questions: 1) How does parental support affect developmental outcomes in preschoolers? 2) How does child temperament affect child emotional development? 3) Does the goodness-of-fit between child temperament and parenting behavior affect children’s internalizing and externalizing behavior? This study used survey and observational data from 112 families (mother, father, 4-year-old child) that participated in The Parents and Preschoolers Study. Measures used in this study included mothers’ and fathers’ observed parenting behavior, child temperament reported by parents, and child internalizing and externalizing behaviors reported by parents. We found that children with high levels of surgency exhibit more externalizing behaviors when mothers choose higher sensitivity parenting behaviors. This contradicted our expectations, as high sensitivity levels in parenting are generally considered to yield positive outcomes. This suggests that parents should choose the parenting style that matches their children’s characteristics, because the mismatch between the child’s temperament and parenting style would lead to challenges in parent-child interactions and the child’s social-emotional development. Education and supportive resources can help parents better understand their children’s temperament.Item Usage of MD protein modeling simulations to quantify results from the novel method of absolute quantitative protein footprinting mass spectrometry(2024-03) Hu, Luke; Cheng, XiaolinThere are currently a couple ways to elucidate 3D protein structures, the 2 current gold standards being nuclear magnetic resonance (NMR) and X-ray crystallography, alongside a new emerging method of cryogenic electron microscopy (Cryo-EM). However, there are many issues associated with these methods that include high overhead, poor suitability to specific groups of proteins, and various other issues. Absolute quantitative protein footprinting mass spectrometry (aqPFMS) is a method recently developed in PI Dr. Hao Chen laboratory at NJIT, taking advantage of electrochemically active residues, surface area exposure of these residues to external solvents, and subsequent ability to covalently bind to certain tags. Our usage of MD simulations is to provide a theoretical comparison to the experimental results for verification. PDB files of Calmodulin bound and unbound from the calcium ion are acquired from a protein database, solvated in a water box, and run through NAMD for 500 ns using computers provided by the Ohio Supercomputer Center. Root-mean-square fluctuations of individual residues (RMSF), and Solvent accessible surface areas (SASA) of lysines are calculated for comparison to the results from the aqPFMS experiments. Once verified, future analysis with this novel technique may be conducted on an alternative configuration of Calmodulin, the Calmodulin-Melitten complex, the SARS-CoV-2 spike protein, and various other proteins.Item Psychosocial Determinants of Immune Reconstitution Post Autologous Stem Cell Transplant Among Patients with Multiple Myeloma(2024-03) Kantaras, Anthony; Christian, LisaThe standard of care for multiple myeloma (MM), an incurable malignancy of plasma, is an autologous stem cell transplant (HSCT). Many MM patients experience significant anxiety, depression, and distress even before reception of ASCT. Such psychological variables are known to lower active immune cell populations, even within healthy individuals. Neutrophils and lymphocytes are two cell populations targeted during HSCTs, serving as indicators of successful engraftment and immune reconstitution. Conversely, overall health status can be exacerbated by environmental factors (e.g., residing in a Medically Underserved Area (MUA)). This study aims to explore how psychosocial variables (depression, anxiety, stress, MUA-categorization) influence clinically relevant outcomes of Absolute Neutrophil Count (ANC) and Total Lymphocyte Count (TLC) in MM patients.Item Investigating the Role of SARS-CoV-2 Nucleocapsid Protein Phosphorylation in Viral Replication(2024-03) Bayachou, Dina; Musier-Forsyth, KarinSARS-CoV-2, the causative agent of COVID-19, is a positive-sense single-stranded betacoronavirus. Significant progress has been made in understanding the SARS-CoV-2 lifecycle. The Nucleocapsid protein (Np) is responsible for viral RNA (vRNA) packaging, plays a vital role in replication and transcription and is associated with viral replication-transcription complexes. Np contains a conserved Ser-Arg (SR)-rich disordered linker between its two structured domains, which is a known site of phosphorylation by multiple host kinases; modification is proposed to regulate its function during infection. Phosphorylated Np has been proposed to participate in viral transcription while non-phosphorylated Np packages gRNA into new virions. However, little is known about Np binding specificity to nucleic acids, and how it is modulated by phosphorylation. The 5’ untranslated region (UTR) of vRNA has conserved secondary structures that are necessary for vRNA replication. We used RNA constructs derived from the SARS-CoV-2 5’UTR containing either stem loops (SLs) 1-4, SL5, or SL1-5, as well as HIV-1 derived RNAs. We also prepared phosphomimetic Np mutants with 3 Ser/Thr to Asp mutations in the N-terminal region of the SR linker (3D1) or the C-terminal region (3D2), as well as a variant with all 6 positions mutated (6D). Direct binding experiments using fluorescence anisotropy (FA) and FA salt-titration binding assays were used to compare salt dependence and binding specificity among non-phosphorylated wild-type and mutant proteins. Trypsin time course digestion was utilized to analyze structural differences between wild-type and mutant proteins as well. Direct binding assays showed that phosphomimetic mutants and non-phosphorylated Np have high-affinity binding (low nM Kd’s) to all RNAs tested. The non-phosphorylated Np protein bound with similar specificity to all SARS and HIV-1 RNAs tested with a strong non-electrostatic component. The 6D phosphomimetic Np mutant displayed high selectivity for SARS RNAs and bound primarily electrostatically with HIV-1 RNAs. The location of the phosphomimetic mutations determined whether binding was primarily electrostatic (3D1) or hydrophobic in nature (3D2). Overall, this data supports the conclusion that the location of phosphorylation within the SR linker of SARS-CoV-2 Np modulates its structure and binding to RNA.Item Non-viral Co-transfection of Plasticity-inducing and β Cell Patterning Transcription Factors Mediates Pro-β Cell Reprogramming in Fibroblast Cultures(2024-03) Gotschall, Andrew; Gallego-Perez, DanielIntroduction: Previously, we have shown that plasmid DNA that encodes transcription factors for β cell patterning (e.g., Pdx1, Ngn3, Mafa) can drive the direct reprogramming of dermal fibroblasts (DFs) into induced β cells (iβCs) with potential to become an alternative method to treat type I diabetes. Recently, our objective has been to investigate whether plasmid DNA that encodes transcription factors for skin plasticity (e.g., Tcf3, Sox9, Trp63) can increase DFs multipotency and, therefore, β cell reprogramming efficiency. Materials and Methods: We identified 3 transcription factors (3SP) for skin cell plasticity and 7 transcription factors (7βC) for β cell development. Bulk electroporation (BEP) was utilized for cell samples of ~1.2 million and nanoelectroporation (NEP) was utilized for cell samples of ~250,000. Combinations of plasmid DNA encoding for 3SP factors or pCMV6 (control plasmid DNA) were delivered to mouse embryonic fibroblasts (MEFs) in vitro using BEP. Combinations of plasmid DNA encoding for 3SP+7βC factors or pCMV6 (control plasmid DNA) were delivered MEFs in vitro using BEP and NEP. Gene and protein expressions were analyzed using qRT-PCR or immunohistology as appropriate. Data was collected and analyzed by blinded investigators using Prism GraphPad and ImageJ. Results: The ability of 3SP to open the chromatin landscape was significant 7 days post-BEP. Furthermore, MEFs transfected with 3SP exhibited decreased fluorescent methylation markers 7 days post-BEP. MEFs transfected with 3SP+7βC transcription factors significantly increased gene expression for both insulin 1 and insulin 2 14 days post-BEP. This increased insulin 1/2 expression correlated with a small population ( < 1%) of transfected cells expressing insulin protein 14 days post-BEP and a larger population (>1%) expressing insulin protein 14 days post-NEP. Conclusion: Our findings suggest that DFs transfected with plasmid DNA encoding for 3SP factors exhibit increased multipotency. Furthermore, DFs transfected with DNA encoding for 3SP+7βC factors have the potential to reprogram into iβCs. Current experimentation includes transcription factor reduction and transition to mouse models. Future development of this alternative cell source to treat and potentially cure type I diabetes could greatly improve quality of life for diabetic patients all over the world.Item The Equitable Impacts of Coaching Reports on Pre-PharmD Students Self-Directed Learning and Pharmaceutical Science Exam Performance(2024-03) Hoffmann, Hannah; Denton, NicholasTitle: Equitable Impacts of Metacognitive Coaching Reports on Undergraduate Students Self-Directed Learning and Pharmaceutical Science Exam Performance Introduction/Background: Disparities persist in STEM retention rates across various demographic factors. The incidence of dropping a STEM major is higher in Black and Latine students. First generation students report not having the same exposure to time management and metacognition-driven study skills as continuous generation students, leading to disparities in examination performance and overall success in college. Methods: Investigators captured exam performance and exit survey data from Bachelors of Science of Pharmaceutical Science (BSPS) students enrolled in a pharmaceutical sciences course from AU19-SP23. AU19-SP20 served as historic controls with 3 mid-stakes, non-cumulative exams. From AU20-SP21, investigators implemented 3 scaffolded semi-cumulative exams with metacognitive coaching reports providing individual content and Bloom's Taxonomy scores. The final iteration then implemented 6 scaffolded low-stakes semi-cumulative exams with metacognitive coaching reports with incorrect question rationales added. Self-reported student demographic data was provided along with learning strategies used after the first module exam. Results: Exam performance scores indicated modest to dramatic improvement in all content areas following the AU21 iteration including metacognitive coaching and low stake exam coaching reports. Pharmaceutics content saw the most dramatic improvement, with >15% increase in correct answers. Student performance improved on categories of Bloom’s Taxonomy, with “Remember” and “Apply” driven questions seeing a 5-10% increase in correct answers. Metacognitive coaching revealed study strategies like randomized, repeat practice and study groups demonstrated increased studying efficiency with higher incidence of students reporting earning a satisfactory grade with satisfactory time management. Conclusions: Individualized coaching reports that include both content and Bloom's categories combined with a scaffolded semi-cumulative exam design equitably improves student learning across multiple demographics. Findings suggest that providing coaching reports on 3 levels of Bloom's Taxonomy along with a single metacognition lecture helps students identify limitations to their current learning strategies along with guidance to optimize learning and that scaffolding exams to low stakes at the start (7%) and mid stakes (27%) at the end promotes growth mindset when assessments are more weighed toward final learning. Students benefited from assessing a topic 4-6 times throughout a semester, which provides repeat practice in addition to providing opportunity for students to respond to formative feedback.Item Mechanism Underlying Astrocytic Uptake of Sulforhodamine 101 (SR101)(2024-03) Liu, Xuanting; Zhou, MinSulforhodamine 101 (SR101) is a commonly used chemical marker for astrocytes and is particularly useful in functional in vivo and in situ studies. However, the mechanism underlying the astrocytic uptake of SR101 remains elusive. Serendipitously, we found that SR101 uptake can be fully inhibited by meclofenamic acid (MFA). The MFA-mediated SR101 uptake inhibition is characterized by a non-competitive binding of MFA to the SR101 uptake pathway, a rapid inhibitory time course (T50,0.499 min), and high efficacy (EC50, 6.3631 μM). Therefore, MFA emerges as a useful inhibitor to further explore the mechanism of SR101 uptake in astrocytes.