Roundabouts: A Study in Green

The purpose of this project was to provide insight on the subject of the implementation of roundabouts as an alternative to traditional intersections. Specifically, this project focuses primarily on intersection improvement projects performed by the City of Green, a municipality local to Akron, Ohio. The report discusses many of the considerations that contributed to roundabout conversion being established as the preferred improvement for the State Route 619-Pickle Rd and State Route 619-Myersville Rd intersections located within the City of Green, along with additional details pertaining to these two public projects (completed in 2018 and 2019 respectively). The intent of this research is that it be an instructive resource for developing a more comprehensive understanding of the thought processes associated with intersection improvement via roundabout conversion

On Performance Discrepancies Across Local Homophily Levels in Graph Neural Networks

Research on GNNs has highlighted a relationship between high homophily (i.e., the tendency for nodes of a similar class to connect) and strong predictive performance in node classification. However, recent research has found the relationship to be more nuanced, demonstrating that even simple GNNs can learn in certain heterophilous settings. To bridge the gap between these findings, we revisit the assumptions made in previous works and identify that datasets are often treated as having a constant homophily level across nodes. To align closer to real-world datasets, we theoretically and empirically study the performance of GNNs when the local homophily level of a node deviates at test-time from the global homophily level of its graph. To aid our theoretical analysis, we introduce a new parameter to the preferential attachment model commonly used in homophily analysis to enable the control of local homophily levels in generated graphs, enabling a systematic empirical study on how local homophily can impact performance. We additionally perform a granular analysis on a number of real-world datasets with varying global homophily levels. Across our theoretical and empirical results, we find that (a)~ GNNs can fail to generalize to test nodes that deviate from the global homophily of a graph, (b)~ high local homophily does not necessarily confer high performance for a node, and (c)~ GNN models designed to handle heterophily are able to perform better across varying heterophily ranges irrespective of the dataset's global homophily. These findings point towards a GNN's over-reliance on the global homophily used for training and motivates the need to design GNNs that can better generalize across large local homophily ranges

A theoretical model of cytokinesis implicates feedback between membrane curvature and cytoskeletal organization in asymmetric cytokinetic furrowing

During cytokinesis, the cell undergoes a dramatic shape change as it divides into two daughter cells. Cell shape changes in cytokinesis are driven by a cortical ring rich in actin filaments and nonmuscle myosin II. The ring closes via actomyosin contraction coupled with actin depolymerization. Of interest, ring closure and hence the furrow ingression are nonconcentric (asymmetric) within the division plane across Metazoa. This nonconcentricity can occur and persist even without preexisting asymmetric cues, such as spindle placement or cellular adhesions. Cell-autonomous asymmetry is not explained by current models. We combined quantitative high-resolution live-cell microscopy with theoretical modeling to explore the mechanistic basis for asymmetric cytokinesis in the Caenorhabditis elegans zygote, with the goal of uncovering basic principles of ring closure. Our theoretical model suggests that feedback among membrane curvature, cytoskeletal alignment, and contractility is responsible for asymmetric cytokinetic furrowing. It also accurately predicts experimental perturbations of conserved ring proteins. The model further suggests that curvature-mediated filament alignment speeds up furrow closure while promoting energy efficiency. Collectively our work underscores the importance of membrane–cytoskeletal anchoring and suggests conserved molecular mechanisms for this activity

Mammary Tissue-Derived Extracellular Matrix Hydrogels Reveal the Role of the Irradiated Microenvironment in Breast Cancer Recurrence

Radiation therapy (RT) is essential for triple negative breast cancer (TNBC) treatment. However, patients with TNBC continue to experience recurrence after RT. Extracellular matrix (ECM) alternations in healthy breast tissue induced by radiation and its role in tumor recurrence are still unknown. In this study, we evaluated the structure, molecular composition, and mechanical properties of irradiated murine mammary fat pads (MFPs) and developed ECM hydrogels from decellularized tissues to assess the effects of RT-induced ECM changes on breast cancer cell behavior. Irradiated MFPs were characterized by increased ECM deposition and fiber density compared to unirradiated controls, which may provide a platform for cell invasion and proliferation. ECM component changes in collagens I, IV, and VI, and fibronectin were observed following irradiation. Encapsulated TNBC cell proliferation was enhanced in irradiated ECM hydrogels, and morphology analysis indicated an increase in invasive capacity. In addition, TNBC cells co-cultured with macrophages in irradiated ECM hydrogels exhibited further increases in cell proliferation. Our study establishes that the ECM in the irradiated microenvironment promotes TNBC invasion and proliferation that is enhanced in the presence of macrophages. This work represents an important step toward elucidating how changes in the ECM after RT contribute to breast cancer recurrence.This is a pre-print of the article Zhu, Tian, Steven M. Alves, Ariana Adamo, Xiaona Wen, Kevin C. Corn, Anastasia Shostak, Nicholas D. Shaub et al. "Mammary Tissue-Derived Extracellular Matrix Hydrogels Reveal the Role of the Irradiated Microenvironment in Breast Cancer Recurrence." bioRxiv (2022). DOI: 10.1101/2022.05.16.492117. Copyright 2022 The Authors. Posted with permission

A theoretical model of cytokinesis implicates feedback between membrane curvature and cytoskeletal organization in asymmetric cytokinetic furrowing

During cytokinesis, the cell undergoes a dramatic shape change as it divides into two daughter cells. Cell shape changes in cytokinesis are driven by a cortical ring rich in actin filaments and nonmuscle myosin II. The ring closes via actomyosin contraction coupled with actin depolymerization. Of interest, ring closure and hence the furrow ingression are nonconcentric (asymmetric) within the division plane across Metazoa. This nonconcentricity can occur and persist even without preexisting asymmetric cues, such as spindle placement or cellular adhesions. Cell-autonomous asymmetry is not explained by current models. We combined quantitative high-resolution live-cell microscopy with theoretical modeling to explore the mechanistic basis for asymmetric cytokinesis in the Caenorhabditis elegans zygote, with the goal of uncovering basic principles of ring closure. Our theoretical model suggests that feedback among membrane curvature, cytoskeletal alignment, and contractility is responsible for asymmetric cytokinetic furrowing. It also accurately predicts experimental perturbations of conserved ring proteins. The model further suggests that curvature-mediated filament alignment speeds up furrow closure while promoting energy efficiency. Collectively our work underscores the importance of membrane–cytoskeletal anchoring and suggests conserved molecular mechanisms for this activity