University of Wisconsin Madison College of Engineering

Biomedical Engineering Seminar Series

The Department of Biomedical Engineering Seminar Series consists of presentations on current research topics of interest to biomedical engineering graduate students and faculty by on-campus and visiting engineers and scientists.


Biomedical Engineering Spring 2013 Seminar Program

 

Date

Topic

Speaker

Monday
1/28/2013

From the Dynamics of Sand to the Dynamics of Robots: Using Advanced Computing in Virtual Prototyping for Better Engineering Designs
(Abstract)

Prof. Dan Negrut
Director, Wisconsin Applied Computer Center Dept. of Mechanical Engineering Dept. of Electrical and Computer Engineering
UW - Madison

Monday
2/18/2013

Hilldale Distinguished Lecturer
Simple building blocks of complex biological systems
(Abstract)

Prof. Uri Alon
Weizmann Institute of Science
Rehovot, Israel

Monday
2/25/2013

Hypofractionated Radiotherapy and the Real Issue: Oxygen Dynamics
(Abstract)

Prof. Michael Kissick
Medical Physics, Human Oncology, and affiliated with the Morgridge Institute for Research
UW-Madison

Monday
3/4/2013

University Distinguished Lecturer
MR-guided interventions and thermal therapy
(Abstract)

Prof. Jason Stafford
Dept. of Biomedical Engineering
University of Texas Health Sciences Center and MD Anderson Cancer Center, Houston, TX

Monday
3/11/2013

Computational models to investigate anti-angiogenic cancer therapies targeting the VEGF pathway
(Abstract)

Dr. Stacey Finley
Postdoctoral Fellow under Prof. Popel, Dept. of Biomedical Engineering, School of Medicine
Johns Hopkins University

Monday
3/18/2013

Novel pathways for cardiac matrix assembly
(Abstract)
Cosponsored by LOCI and Prairie Technologies

Prof. Alissa Weaver
School of Medicine,
Vanderbilt University
Nashville, TN

Monday
4/15/2013

Systems analysis of TGF-beta signaling dynamics
(Abstract)
Sponsored by UWCCC

Prof. Xuedong Liu
Dept. of Chemistry and Biochemistry
University of Colorado, Boulder

Monday
4/22/2013

Glucose effects on endothelial cell mechanotransduction
(Abstract)

Prof. Alisa Morss Clyne
Dept. of Mechanical Engineering
Drexel University,
Philadelphia, PA

Monday
4/29/2013

Big Ten Speaker
The importance of multiscale mechanics in tissue engineering and mechanobiology
(Abstract)

Prof. Ed Sander
Dept. of Biomedical Engineering
University of Iowa,
Iowa City, Iowa

Monday
5/6/2013

Continuing professional development in an academic medical center: a maintenance of quality issue
(Abstract)

Prof. Carla Pugh
Dept. of Surgery
UW-Madison

 

 

Abstract, 1/28/2013
From the Dynamics of Sand to the Dynamics of Robots: Using Advanced Computing in Virtual Prototyping for Better Engineering Designs
Prof. Dan Negrut

This talk outlines a high performance computing-enabled software infrastructure aimed at supporting physics-based simulation for virtual prototyping purposes. The motivation for building this infrastructure is a desire to understand and shape the role that advanced computing can play in Computer Aided Engineering over the next decade. The applications we take upon are related to granular dynamics, rigid/flexible many-body dynamics, and fluid-solid interaction problems. CHRONO, the software infrastructure developed as part of this ongoing effort, partitions the problem of interest into a number of sub-problems that are solved in parallel using Graphics Processing Unit (GPU) cards, or multi-core CPUs. The five components at the cornerstone of the vision that eventually led to CHRONO are: (a) modeling support for multi-physics phenomena; (b) scalable numerical methods for multi-GPU and multi-core hardware architectures; (c) methods for proximity computation and collision detection; (d) support for domain decomposition and load balance; and (e) tools for carrying out visualization and post-processing in a distributed manner. Several engineering applications will be used to demonstrate how these five components are implemented to leverage a heterogeneous CPU/GPU cluster. The talk will conclude with a brief discussion of current trends in high performance computing and how they are poised to change the field of Computational Science in the near future.

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Abstract, 2/18/2013
Simple building blocks of complex biological systems
Prof. Uri Alon


To understand biological systems, our lab has defined "network motifs": basic interaction patterns that recur throughout biological networks, much more often than expected at random. The same small set of network motifs appears to serve as the building blocks of the circuitry that processes information from bacteria to mammals. Specific network motifs may be universal building blocks of biological computation. We experimentally studied the function of each network motif in the bacterium E. coli using dynamic fluorescent measurements from living cells. Each network motif can serve as an elementary circuit with a defined function: filters, pulse generators, response accelerators, temporal-pattern generators and more. Evolution seems to have rediscovered the same motifs again and again, perhaps because they are the simplest and most robust circuits that perform these information-processing functions.

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Abstract, 2/25/2013
Hypofractionated Radiotherapy and the Real Issue: Oxygen Dynamics
Prof. Michael Kissick


Radiation therapy goes all the way back to Mme. Curie. The main physics-related advances are reaching the point of diminishing returns. Being able to sculpt the beam and adjust it for motion are now so advanced that sparing the normal tissue around a tumor is nearly optimal from a physics/geometrical standpoint. Breaking the treatment up into many "fractions" to integrate damage in the tumor while allowing normal tissue to repair may not be as needed as before. If that is the case, the effects of oxygen dynamics can become much more challenging. In these hypofractionated treatments expected to be more common in the future, we will need to monitor and adapt to oxygen transients much better than we do now. I believe optical technologies can play a key role.

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Abstract, 3/4/2013
MR-guided interventions and thermal therapy
Prof. Jason Stafford


The unique soft-tissue contrast and functional imaging capabilities make MRI an attractive modality for planning, targeting, monitoring and verifying successful completion of diagnostic and therapeutic interventions.Image-guidance of minimally invasive interventions for diagnosis and therapy has been a rapidly evolving, multidisciplinary field, particularly with respect to incorporation of increasing advanced imaging equipment for the planning, targeting, monitoring and assessment of procedures. Traditionally, these vascular, therapeutic and biopsy procedures have been carried out using fluoroscopy, ultrasound or CT. MRI is an inherently 3D, non-ionizing imaging modality offering multiple soft-tissue contrast mechanisms as well as functional imaging in a single locale. Because of these unique properties, use of MRI for guidance of interventions has been of growing interest in recent years for a number of procedures requiring stereotactic localization and planning or real-time image guidance and monitoring, such as biopsy and thermal therapy delivery.

However, despite the recent proliferation of commercially available hardware and software solutions for MR guided procedures, integration of MRI into an intraoperative and interventional environment remains a challenge. Because of the cost associated with equipment acquisition and siting, careful attention should be paid to specifying the MR system as well as the location of the facility. The specification of hardware and software, as well as the layout of the suite, strongly influence workflow and domain of possible procedures that can be realistically performed in the suite. Last, but certainly not least, the safety of patients and staff working in the MR environment must be considered and programs put in place to continuously educate staff who work in these suites.

This talk aims to provide an overview of MR-guided interventional procedures which are currently performed clinically on high-field (>1.5T) cylindrical bore systems with an emphasis on the potential for guidance of thermal ablative therapies. Illustrations of the use of MRI for planning and targeting lesions as well as monitoring and assessing thermal therapy delivery (i.e., cryotherapy and laser ablation) will be presented and challenges associated with these procedures discussed.

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Abstract, 3/11/2013
Computational models to investigate anti-angiogenic cancer therapies targeting the VEGF pathway
Dr. Stacey Finley


Angiogenesis, the formation of new blood vessels from pre-existing vasculature, is a tightly regulated biological process involved in physiological function such as wound healing and exercise, as well as in pathological conditions, including preeclampsia, ischemic heart disease, and cancer. Inducing angiogenesis is a hallmark of cancer, as tumors cannot grow beyond 1 mm in diameter without eliciting the formation of blood capillaries to supply oxygen and other nutrients. Vascular endothelial growth factor (VEGF) is a key regulator of angiogenesis and its role in cancer biology has been widely studied. Given the action of VEGF in promoting angiogenesis, it has been targeted in various cancer treatments.

Systems biology approaches, including experiment-based computational modeling, are useful in gaining insight into the complexity of tumor angiogenesis. These models provide a framework to test biological hypotheses and optimize effective therapies that aim to inhibit tumor vascularization and growth. Here, I describe the development of whole-body, molecular-detailed compartment models of VEGF kinetics and transport in mice and humans and the application of these models to predict the effect of various anti-angiogenic therapies that inhibit VEGF. The mouse model has been fit to available experimental data and complements pre-clinical drug studies, and the human model is applied to interpret clinical data. Both models reproduce experimental observations and predict the dynamics of VEGF in the body. Importantly, the models simulate the effects of intravenous administration of anti-VEGF agents. The model predictions are relevant to the clinical application of VEGF-targeting therapies and generate testable hypotheses that can aid in elucidating the mechanism of action of anti-VEGF agents. This work is useful for the development and optimization of personalized cancer treatment strategies that target the VEGF pathway.

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Abstract, 3/18/2013
Novel pathways for cardiac matrix assembly
Prof. Alissa Weaver


Extracellular matrix (ECM) secretion and assembly critically contributes to tissue repair and pathophysiologic processes, including cardiac development, and repair of the injured heart. Nonetheless, its deposition by intracellular secretory pathways is not well understood. Recently, we discovered that autocrine secretion of fibronectin (FN) can occur via recycling from a secretory lysosome-like compartment, rather than (or in addition to) the conventional Golgi route. Functionally, this mechanism of matrix recycling promotes efficient and persistent motility of cancer and epicardial cells and is also used for assembly of cell-derived matrices by multiple cell types, including mouse embryonic fibroblasts and cardiac stromal cells. Understanding this novel pathway of matrix assembly may lead to a greater understanding of how extracellular matrix is assembled and remodeled during a variety of tissue conditions.

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Abstract, 4/15/2013
Systems analysis of TGF-beta signaling dynamics
Prof. Xuedong Liu


Transforming growth factor-β (TGF-β) is a prominent signaling pathway crucial for regulating diverse aspects of cellular homeostasis. The physiological responses to TGF-β stimulation are diverse and vary amongst different cell types and environmental conditions. The principal molecular components of TGF-β signaling have been identified yet this knowledge is insufficient to fully account for the known biology. Understanding TGF-β signaling complexity will require adopting a system view of cell function in which the discovery of new molecules and connections is combined with studies of system dynamics. Our research has been focused on understanding the quantitative basis for how TGF-β signals are transduced into both canonical Smad and non-canonical Smad-independent pathway kinetics. Using a combined experimental and modeling approach, we analyzed how cells read TGF-β concentration with high precision to produce different biological responses and demonstrated that the duration and amplitude of cellular response depend on ligand dose. TGF-β ligand depletion can be the principal determinant of the Smad signal duration and account for long term ultrasensitive response to TGF-β signaling. Finally, how TGF-β modulates MAPK signaling networks to regulate coordinated and individual cell migration in epithelial sheets will be discussed.

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Abstract, 4/22/2013
Glucose effects on endothelial cell mechanotransduction
Prof. Alisa Morss Clyne


In a healthy blood vessel, endothelial cells dynamically integrate biomechanical and biochemical signals from the flowing blood at their apical surface and the basement membrane at their basolateral surface. In disease, changes in the biochemical environment may disturb endothelial cell response to mechanical forces, and the mechanical environment may affect biochemical transport, binding, and signaling. In this talk, I will present our research demonstrating that altered blood glucose, such as that experienced by people with diabetes, disturbs endothelial cell response to shear stress and cyclic strain. I will then describe computational and experimental models of fluid flow effects on fibroblast growth factor-2 transport, binding, and signaling, and the impact of this work on drug delivery. Finally, I will show our recent research investigating how substrate stiffness affects endothelial cell migration, as well as a new device we are developing to dynamically measure both cell stiffness and mechanotransduction. This research highlights applications of biomechanical engineering to understand, diagnose, and treat cardiovascular disease.

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Abstract, 4/29/2013
The importance of multiscale mechanics in tissue engineering and mechanobiology
Prof. Ed Sander


Multiscale mechanical interactions are scale spanning physical interactions between the tissue and the extracellular matrix (ECM). They are involved in a variety of biological phenomena, including tissue growth, remodeling, disease, and damage. These interactions are important to characterize because they control both the mechanical behavior of the tissue and the manner in which mechanical signals are propagated to the cellular level - issues that are particularly important to tissue engineering applications. In this seminar, I will discuss my work with engineered tissues and how developing multiscale computer models can help us better understand these multiscale processes. In doing so, we can devise better protocols for producing functional engineered tissues, as well as understanding the role of these processes in other biological contexts, such as wound healing and disease. An essential component for moving this work forward is the continued development of the physics of cell-ECM interactions from direct observations and image analysis.


Biography: Ed Sander is an assistant professor in the Department of Biomedical Engineering at the University of Iowa. During his postdoctoral training, he was a research associate at the Cincinnati Shriners Hospital for Children and the Department of Surgery at the University of Cincinnati, and an NIH NRSA postdoctoral fellow in the Department of Biomedical Engineering at the University of Minnesota. He obtained his B.S. in Chemical Engineering from the University of Texas at Austin, and his M.Eng. and Ph.D. in Biomedical Engineering from Tulane University.

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Abstract, 5/6/2013
Continuing professional development in an academic medical center: a maintenance of quality issue
Prof. Carla Pugh


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