Ernesto Augusto Bueno da Fonseca Lima

Ernesto Augusto Bueno da Fonseca Lima

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Research Focus & Metrics

Academic Career Length

12Years (2015-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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17 May 2022 in Biophysics Reviews
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CWChengyue Wu
Chengyue Wu
GLGuillermo Lorenzo
Guillermo Lorenzo
DIDavid A. Hormuth, II
David A. Hormuth, II
ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
KSKalina Polet Slavkova
Kalina Polet Slavkova
TYThomas E. Yankeelov
Thomas E. Yankeelov
Digital twins employ mathematical and computational models to virtually represent a physical object (e.g., planes and human organs), predict the behavior of the object, and enable decision-making to optimize the future behavior of the object. While digital twins have been widely used in engineering for decades, their applications to oncology are only just emerging. Due to advances in experimental techniques quantitatively characterizing cancer, as well as advances in the mathematical and computational sciences, the notion of building and applying digital twins to understand tumor dynamics and personalize the care of cancer patients has been increasingly appreciated. In this review, we present the opportunities and challenges of applying digital twins in clinical oncology, with a particular focus on integrating medical imaging with mechanism-based, tissue-scale mathematical modeling. Specifically, we first introduce the general digital twin framework and then illustrate existing applications of image-guided digital twins in healthcare. Next, we detail both the imaging and modeling techniques that provide practical opportunities to build patient-specific digital twins for oncology. We then describe the current challenges and limitations in developing image-guided, mechanism-based digital twins for oncology along with potential solutions. We conclude by outlining five fundamental questions that can serve as a roadmap when designing and building a practical digital twin for oncology and attempt to provide answers for a specific application to brain cancer. We hope that this contribution provides motivation for the imaging science, oncology, and computational communities to develop practical digital twin technologies to improve the care of patients battling cancer.

5 August 2019 in PLOS Biology
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Journal Article
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KJKaitlyn E. Johnson
Kaitlyn E. Johnson
GHGrant Howard
Grant Howard
WMWilliam Mo
William Mo
MSMichael K. Strasser
Michael K. Strasser
ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
ABAmy Brock
Amy Brock
Most models of cancer cell population expansion assume exponential growth kinetics at low cell densities, with deviations to account for observed slowing of growth rate only at higher densities due to limited resources such as space and nutrients. However, recent preclinical and clinical observations of tumor initiation or recurrence indicate the presence of tumor growth kinetics in which growth rates scale positively with cell numbers. These observations are analogous to the cooperative behavior of species in an ecosystem described by the ecological principle of the Allee effect. In preclinical and clinical models, however, tumor growth data are limited by the lower limit of detection (i.e., a measurable lesion) and confounding variables, such as tumor microenvironment, and immune responses may cause and mask deviations from exponential growth models. In this work, we present alternative growth models to investigate the presence of an Allee effect in cancer cells seeded at low cell densities in a controlled in vitro setting. We propose a stochastic modeling framework to disentangle expected deviations due to small population size stochastic effects from cooperative growth and use the moment approach for stochastic parameter estimation to calibrate the observed growth trajectories. We validate the framework on simulated data and apply this approach to longitudinal cell proliferation data of BT-474 luminal B breast cancer cells. We find that cell population growth kinetics are best described by a model structure that considers the Allee effect, in that the birth rate of tumor cells increases with cell number in the regime of small population size. This indicates a potentially critical role of cooperative behavior among tumor cells at low cell densities with relevance to early stage growth patterns of emerging and relapsed tumors.

25 October 2016 in Mathematical Models and Methods in Applied Sciences
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ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
JOJ. T. Oden
J. T. Oden
DIDavid A. Hormuth, II
David A. Hormuth, II
TYThomas Yankeelov
Thomas Yankeelov
RARegina Almeida
Regina Almeida

1 December 2017 in Computer Methods in Applied Mechanics and Engineering
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Journal Article
Closed access
ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
JOJ.T. Oden
J.T. Oden
BWBarbara Wohlmuth
Barbara Wohlmuth
ASA. Shahmoradi
A. Shahmoradi
DIDavid A. Hormuth, II
David A. Hormuth, II
THT. Horger
T. Horger

Verified
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AJAngela Jarrett
Angela Jarrett
DFDanial Faghihi
Danial Faghihi
DIDavid A. Hormuth, II
David A. Hormuth, II
ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
JVJohn Virostko
John Virostko
TYThomas Yankeelov
Thomas Yankeelov
Optimal control theory is branch of mathematics that aims to optimize a solution to a dynamical system. While the concept of using optimal control theory to improve treatment regimens in oncology is not novel, many of the early applications of this mathematical technique were not designed to work with routinely available data or produce results that can eventually be translated to the clinical setting. The purpose of this review is to discuss clinically relevant considerations for formulating and solving optimal control problems for treating cancer patients. Our review focuses on two of the most widely used cancer treatments, radiation therapy and systemic therapy, as they naturally lend themselves to optimal control theory as a means to personalize therapeutic plans in a rigorous fashion. To provide context for optimal control theory to address either of these two modalities, we first discuss the major limitations and difficulties oncologists face when considering alternate regimens for their patients. We then provide a brief introduction to optimal control theory before formulating the optimal control problem in the context of radiation and systemic therapy. We also summarize examples from the literature that illustrate these concepts. Finally, we present both challenges and opportunities for dramatically improving patient outcomes via the integration of clinically relevant, patient-specific, mathematical models and optimal control theory.

10 April 2020 in PLOS ONE
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Journal Article
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CPCaleb M. Phillips
Caleb M. Phillips
ELErnesto Augusto Bueno da Fonseca Lima
Ernesto Augusto Bueno da Fonseca Lima
RWRyan T. Woodall
Ryan T. Woodall
ABAmy Brock
Amy Brock
TYThomas E. Yankeelov
Thomas E. Yankeelov
Tumor associated angiogenesis is the development of new blood vessels in response to proteins secreted by tumor cells. These new blood vessels allow tumors to continue to grow beyond what the pre-existing vasculature could support. Here, we construct a mathematical model to simulate tumor angiogenesis by considering each endothelial cell as an agent, and allowing the vascular endothelial growth factor (VEGF) and nutrient fields to impact the dynamics and phenotypic transitions of each tumor and endothelial cell. The phenotypes of the endothelial cells (i.e., tip, stalk, and phalanx cells) are selected by the local VEGF field, and govern the migration and growth of vessel sprouts at the cellular level. Over time, these vessels grow and migrate to the tumor, forming anastomotic loops to supply nutrients, while interacting with the tumor through mechanical forces and the consumption of VEGF. The model is able to capture collapsing and breaking of vessels caused by tumor-endothelial cell interactions. This is accomplished through modeling the physical interaction between the vasculature and the tumor, resulting in vessel occlusion and tumor heterogeneity over time due to the stages of response in angiogenesis. Key parameters are identified through a sensitivity analysis based on the Sobol method, establishing which parameters should be the focus of subsequent experimental efforts. During the avascular phase (i.e., before angiogenesis is triggered), the nutrient consumption rate, followed by the rate of nutrient diffusion, yield the greatest influence on the number and distribution of tumor cells. Similarly, the consumption and diffusion of VEGF yield the greatest influence on the endothelial and tumor cell numbers during angiogenesis. In summary, we present a hybrid mathematical approach that characterizes vascular changes via an agent-based model, while treating nutrient and VEGF changes through a continuum model. The model describes the physical interaction between a tumor and the surrounding blood vessels, explicitly allowing the forces of the growing tumor to influence the nutrient delivery of the vasculature.