Endothelial cell phenotypic behaviors cluster into dynamic state transition programs modulated by angiogenic and angiostatic cytokines

Angiogenesis requires coordinated dynamic regulation of multiple phenotypic behaviors of endothelial cells in response to environmental cues. Multi-scale computational models of angiogenesis can be useful for analyzing effects of cell behaviors on the tissue level outcome, but these models require more intensive experimental studies dedicated to determining the required quantitative “rules” for cell-level phenotypic responses across a landscape of pro- and anti-angiogenic stimuli in order to ascertain how changes in these single cell responses lead to emerging multi-cellular behavior such as sprout formation. Here we employ single-cell microscopy to ascertain phenotypic behaviors of more than 800 human microvascular endothelial cells under various combinational angiogenic (VEGF) and angiostatic (PF4) cytokine treatments, analyzing their dynamic behavioral transitions among sessile, migratory, proliferative, and apoptotic states. We find that an endothelial cell population clusters into an identifiable set of a few distinct phenotypic state transition patterns (clusters) that is consistent across all cytokine conditions. Varying the cytokine conditions, such as VEGF and PF4 combinations here, modulates the proportion of the population following a particular pattern (referred to as phenotypic cluster weights) without altering the transition dynamics within the patterns. We then map the phenotypic cluster weights to quantified population level sprout densities using a multi-variate regression approach, and identify linear combinations of the phenotypic cluster weights that associate with greater or lesser sprout density across the various treatment conditions. VEGF-dominant cytokine combinations yielding high sprout densities are characterized by high proliferative and low apoptotic cluster weights, whereas PF4-dominant conditions yielding low sprout densities are characterized by low proliferative and high apoptotic cluster weights. Migratory cluster weights show only mild association with sprout density outcomes under the VEGF/PF4 conditions and the sprout formation characteristics explored here.National Science Foundation (U.S.) (NSF grant EFRI-0735007)National Institutes of Health (U.S.) (NIH grant R01-GM081336)National Institutes of Health (U.S.) (NIH grant R01-EB010246

Engineering of In Vitro 3D Capillary Beds by Self-Directed Angiogenic Sprouting

In recent years, microfluidic systems have been used to study fundamental aspects of angiogenesis through the patterning of single-layered, linear or geometric vascular channels. In vivo, however, capillaries exist in complex, three-dimensional (3D) networks, and angiogenic sprouting occurs with a degree of unpredictability in all x,y,z planes. The ability to generate capillary beds in vitro that can support thick, biological tissues remains a key challenge to the regeneration of vital organs. Here, we report the engineering of 3D capillary beds in an in vitro microfluidic platform that is comprised of a biocompatible collagen I gel supported by a mechanical framework of alginate beads. The engineered vessels have patent lumens, form robust ~1.5 mm capillary networks across the devices, and support the perfusion of 1 µm fluorescent beads through them. In addition, the alginate beads offer a modular method to encapsulate and co-culture cells that either promote angiogenesis or require perfusion for cell viability in engineered tissue constructs. This laboratory-constructed vascular supply may be clinically significant for the engineering of capillary beds and higher order biological tissues in a scalable and modular manner.Singapore-MIT Alliance for Research and Technolog

Single cell decisions in endothelial population in the context of inflammatory angiogenesis

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 161-171).Normalizing angiogenesis is a promising strategy for treatments of cancer and several disorders plagued by misregulated blood supplies. To address the daunting complexity of angiogenesis arising from multiple phenotypic behaviors governed by multiple stimuli, computational approaches have been developed to predict sprouting angiogenic outcomes. In recent years, the agent based model, in which individual cells are modeled as autonomous decision making entities, has become an important tool for simulating complex phenomena including angiogenesis. The reliability of these models depends on model validation by quantitative experimental characterization of the cellular (agent) behaviors which so far has been lacking. To this end, I develop an experimental and computational method to semi-automatically estimate parameters describing the single-cell decision in the agent based model based on flow cytometry aggregate headcount data and single cell microscopy which yields full panel single cell trajectories of individual endothelial cells. Applying thees method to the single cell decision data, I propose two conceptual models to account for the different state transition patterns and how they are modulated in the presence of opposing inflammatory cytokines. The observed unique state transition patterns in the angiogenic endothelial cell population are consistent with one of these descriptions, the diverse population model (DPM). The DPM interpretation offers an alternative view from the traditional paradigm of cell population heterogeneity. This understanding is important in designing appropriate therapeutic agents that take effect at the cellular level to meet a tissue level therapeutic goal.by Tharathorn Rimchala.Ph.D

RE2^2: Region-Aware Relation Extraction from Visually Rich Documents

Current research in form understanding predominantly relies on large pre-trained language models, necessitating extensive data for pre-training. However, the importance of layout structure (i.e., the spatial relationship between the entity blocks in the visually rich document) to relation extraction has been overlooked. In this paper, we propose REgion-Aware Relation Extraction (RE$^2$) that leverages region-level spatial structure among the entity blocks to improve their relation prediction. We design an edge-aware graph attention network to learn the interaction between entities while considering their spatial relationship defined by their region-level representations. We also introduce a constraint objective to regularize the model towards consistency with the inherent constraints of the relation extraction task. Extensive experiments across various datasets, languages and domains demonstrate the superiority of our proposed approach.Comment: NAACL 202

Vascular Endothelial Growth Factor (VEGF) and Platelet (PF-4) Factor 4 Inputs Modulate Human Microvascular Endothelial Signaling in a Three-Dimensional Matrix Migration Context

The process of angiogenesis is under complex regulation in adult organisms, particularly as it often occurs in an inflammatory post-wound environment. As such, there are many impacting factors that will regulate the generation of new blood vessels which include not only pro-angiogenic growth factors such as vascular endothelial growth factor, but also angiostatic factors. During initial postwound hemostasis, a large initial bolus of platelet factor 4 is released into localized areas of damage before progression of wound healing toward tissue homeostasis. Because of its early presence and high concentration, the angiostatic chemokine platelet factor 4, which can induce endothelial anoikis, can strongly affect angiogenesis. In our work, we explored signaling crosstalk interactions between vascular endothelial growth factor and platelet factor 4 using phosphotyrosine-enriched mass spectrometry methods on human dermal microvascular endothelial cells cultured under conditions facilitating migratory sprouting into collagen gel matrices. We developed new methods to enable mass spectrometry-based phosphorylation analysis of primary cells cultured on collagen gels, and quantified signaling pathways over the first 48 h of treatment with vascular endothelial growth factor in the presence or absence of platelet factor 4. By observing early and late signaling dynamics in tandem with correlation network modeling, we found that platelet factor 4 has significant crosstalk with vascular endothelial growth factor by modulating cell migration and polarization pathways, centered around P38α MAPK, Src family kinases Fyn and Lyn, along with FAK. Interestingly, we found EphA2 correlational topology to strongly involve key migration-related signaling nodes after introduction of platelet factor 4, indicating an influence of the angiostatic factor on this ambiguous but generally angiogenic signal in this complex environment.National Science Foundation (U.S.) (NSF EFRI grant 735997)National Institutes of Health (U.S.) (NIH Cell Migration Consortium grant GM06346)National Institutes of Health (U.S.) (NIH Cell Decision Processes Center grant GM68762)National Institutes of Health (U.S.) (NIH grant GM69668)National Institutes of Health (U.S.) (NIH grant GM81336

Food Eating, Entertainment and Distribution Kitchen

The goal of this Interactive Qualifying Project is to design a food truck that is able to provide food for 500 people per day. It has to present an aspect of entertainment, and be aesthetically pleasing. Food truck operators are forced to work in a cramped environment throughout their working day. Most food trucks today do not provide any level of entertainment and are not aesthetically pleasing. For a better working environment for operators, an expanding mechanism is incorporated into the food truck, in which the passenger side of the food truck expands outward when it is in the operating condition. A higher profile mobile kitchen is more likely to become noticed by pedestrians walking by. This food truck design will be the next step in the evolution of mobile kitchens

Artificial Reversible Skin

This project aims to improve the realism of medical simulation mannequins by developing an adaptable system for the skin that is capable of displaying physiological changes in the skin caused by conscious and unconscious perturbations. A design of an artificial skin is developed, which uses organic light emitting diode (OLED) displays implanted underneath the skin of a medical simulation mannequin. After performing fatigue analysis and constructing a proof of concept, it is shown that the use of strategically placed displays can realistically simulate color changes similar to the human physiology

PRINCE: Provider-side Interpretability with Counterfactual Explanations in Recommender Systems

International audienceInterpretable explanations for recommender systems and other machine learning models are crucial to gain user trust. Prior works that have focused on paths connecting users and items in a heterogeneous network have several limitations, such as discovering relationships rather than true explanations, or disregarding other users' privacy. In this work, we take a fresh perspective, and present Prince: a provider-side mechanism to produce tangible explanations for end-users, where an explanation is defined to be a set of minimal actions performed by the user that, if removed, changes the recommendation to a different item. Given a recommendation, Prince uses a polynomial-time optimal algorithm for finding this minimal set of a user's actions from an exponential search space, based on random walks over dynamic graphs. Experiments on two real-world datasets show that Prince provides more compact explanations than intuitive baselines, and insights from a crowdsourced user-study demonstrate the viability of such action-based explanations. We thus posit that Prince produces scrutable, actionable, and concise explanations, owing to its use of counterfactual evidence, a user's own actions, and minimal sets, respectively