I. Lanza, A. Matveyenko (Fall, Winter, Spring) – This course takes an integrated approach to lead students to a deeper understanding of fundamental concepts in human physiology. The goal is to foster critical thinking about how organ systems normally work, and to gain fundamental insight into processes that contribute to disease states. A combination of didactic instruction and learner-centered approaches are used to engage students in understanding structural and functional concepts from cell to organism. This 6 credit course spans 3 quarters. The topics in the first quarter will initially focus on key foundational principles of cellular physiology, followed by the nervous system and renal physiology. In quarter 2, topics will include gastrointestinal, endocrine, and reproductive, and immune systems, again with emphasis on anatomical and functional concepts that drive normal physiology and pathophysiological underpinnings of major diseases/disorders. The third quarter will explore the respiratory, cardiovascular, and musculoskeletal systems. Student evaluations will involve graded quizzes and exams based on assigned readings and information covered during faculty-guided sessions. Student engagement and participation in discussions will also be taken into consideration during evaluation.

M. Urban, S. Leng (Fall, Winter, Spring) – This course will provide an introduction to the fundamental concepts related to medical imaging and biomedical signal processing with a quantitative emphasis. Concepts related to acquisition of biological signals and analysis related to time-domain and frequency-domain evaluation of signals in multiple dimensions will be covered. Diagnostic imaging modalities including radiographic imaging, x-ray computed tomography, digital radiography, nuclear medicine, magnetic resonance imaging, and ultrasound will be covered.

J. Lujan, K. Zhao (Fall, Winter, Spring) – This course provides an overview of the application of engineering principles to address biomedical problems. It focuses on how engineering concepts and techniques can be utilized to solve biomedical challenges and advance healthcare. Through a combination of didactic lectures, case studies, and hands-on projects, students will gain an understanding of various engineering disciplines and their applications in the biomedical field, as well as how to analyze, design, and develop engineering solutions to biomedical problems.

G. Sturchio (Odd: Fall) – An introduction to concepts of radiological health, philosophy and principles of radiation protection, interpretation of standards and regulations, and planning of facilities and activities.

J. Johnson, S. Wan Chan Tseung (Odd: Fall) – This is an introductory graduate course designed for those interested in the radiation sciences. The course will introduce the student to the basic concepts and physical principles that underlie modern radiation physics including atomic structure, radiation, interactions of radiation with matter, introduction to cavity theory, biological effects of radiation (dose), x-ray production and dosimetry techniques.

W. Pawlina (Odd: Winter) – Students dissect selected regions of the human body and learn correct names and locations of associated anatomical structures. Each student then gives a detailed presentation to the class of the region studied.

D. Holmes (Fall) – An introduction to important concepts in applied biomedical imaging, including digital processing of images, image signal characteristics, histogram analysis, domain processing, digital filters, image compression, reconstruction from projections, discussions of image composition, interactive 3D display, image processing and segmentation, registration and quantitative analysis. Practical applications in basic science and medicine are discussed. Students will use ANALYZE biomedical imaging software developed at Mayo to investigate these topics.*offered any quarter if enough students are participating*

This course provides an overview of the mechanical properties and structural behavior of biological tissues. Specific course topics include cell matrix level mechanics, structure and function relationships in tissues and organs, analysis of forces in human function and movement, and application of stress and strain analysis to biological tissues. BMEP 5452 Course Director: Kristen Zhao Term: Winter Prerequisites: None

K. Kaufman (Winter) – This course is an introduction to biomechanics and addresses the fundamental topics of kinematics and kinetics.

D. Dragomir-Daescu (Spring) – This is a combination of in-class teaching and self-directed study to help the students acquire a working knowledge of Finite Element Analysis (FEA). The goal is to teach the fundamental principles using tutorials and computer labs for an accelerated understanding of how the students can use FEA in their specific area of biomedical engineering research.

D. Holmes (Spring) – An introduction to the concepts, methods and applications of image guided technology and interventions, including device tracking, advanced visualizations, workflow emulation and virtual reality simulations in biomedical research and clinical procedures.

S. Riederer (Odd: Spring) – An introduction to physics and engineering aspects of modern diagnostic magnetic resonance imaging (MRI).

M. Joyner (Approval Required) – This course is designed for selected physiology graduate students who seek a broad overview in integrative physiology. The focus will be on presenting broad biological concepts related to integration, regulation, homeostasis, and the multitude of organ systems and how they adapt to various environmental and physical stresses. The course meets once a week for 1½ to 2 hours. It is taught using a collegial problem- solving approach. Students take a major role in where the course goes. The course runs one full academic year. Offered only once per year with consent of instructor required prior to registration.

G. Sturchio (Spring) – Radiation protection philosophy and principles as applied to the medical environment: protection of patients, public, and employees; procedures for obtaining Nuclear Regulatory Commission license. This course has been accredited by the Commission on Accreditation of Medical Physics Education Programs (CAMPEP); please contact the instructor for further information.

N. Remmes, J. Ma, D. Moseley (Winter) – Physics principles of the application of ionizing radiation in radiation therapy, including radiation characteristics, dose calculation, treatment planning/dosimetry, brachytherapy and quality assurance. This course has been accredited by the Commission on Accreditation of Medical Physics Education Programs (CAMPEP); please contact the instructor for further information. Course will not be offered during Winter 2024 quarter; will resume in Winter 2025.

G. Sieck (Approval Required) – This course will provide an understanding of the basic concepts in cell and neurophysiology. The application of current experimental methods and techniques will be emphasized. Classic papers from the literature will be assigned and discussed. Laboratory demonstrations and computer modeling will be included if class size permits.

D. Linden (Fall) – The goal of this course is to provide students the framework to research, present and discuss topics of interest in autonomic neurophysiology.

K. Fatema (Approval Required) – Principles of ultrasound physics and interaction of ultrasound with biological tissues; principles and methods of tissue imaging using ultrasound; evaluating mechanical properties of tissue by ultrasound; measuring blood flow and tissue motion by Doppler method; artifacts in ultrasound imaging and in Doppler techniques; overview of recent and advanced techniques in medical ultrasound clinical applications of ultrasound.

D. Hermes (Spring) - Recent advances in Open Science are resulting in an explosion of openly available data, computational tools and data visualization methods. In this course, students will learn about and become familiar with some data and tools in systems (neuro) biological research. The course will combine lectures with hands on practice, to encourage active learning of reproducible computing practices and help bridge the gap between theory and research. Student evaluations will involve participation on laboratory assignments and student presentations. The course will include a final project that will serve as the final exam

C. Schwarz, A. Manduca (Winter) – Please contact Drs. Schwarz and Manduca if you are planning to take this course, as the course is held is based on student interest. An in-depth study of difficult problems in imaging science as they relate to biomedical images. Areas of study include image segmentation, image registration, texture analysis, shape description and matching, deconvolution, multispectral analysis and denoising. This course is offered based on student interest.

TBA (Approval Required) – Special topics in the imaging sciences applied to biomedical problems and data; including 3-D imaging, volume rendering, surface rendering, image segmentation, image registration and fusion, shape description and analysis, multi-spectral analysis and classification, virtual reality visualization, image modeling.

J. Miller and A. Haak (Approval Required) – Presentations of research topics related to physiology and biomedical engineering. All BMEP students are required to attend seminars. In addition to attendance, students are required to give two short (30 min) presentations related to their own research projects, one prior to the start of winter quarter in their third year and the second in their fifth year. Students should register in the quarter in which they give their second presentation.

D. Holmes, C. Haider (Fall, Winter, Spring) – The Biomedical Engineering Journal Club provides a forum for discussion of recent advances in biomedical engineering and physiology. Development of critical reading and writing skills will be incorporated as they apply to manuscript and grant reviewing and writing. Each student is expected to present at least one paper per year. Faculty will be invited to participate as appropriate. Students are required to attend for 3 consecutive quarters in a given year - fall, winter and spring (register for course in spring).

A. Manduca (Winter) – This course provides an overview of advanced mathematical and numerical methods commonly used in biomedical research including: theory and solution of ordinary and partial differential equations, common transforms, function fitting, interpolation and extrapolation, optimization and search algorithms, and filtering and time series analysis.

T. Kline (Spring) – This course will cover deep learning methods, with particular emphasis on applications in medical imaging. Moderate Python programming skills are required. The course will consist of a series of videos to be viewed on the student’s own time, and classroom time will consist of discussion of principles covered. The course will also include a major project that serves as the “final exam” for the course.

H. Edmonson (Even: Winter) – Introduction to MRI laboratory methods. Firsthand experience in basic and advanced MR image acquisition strategies, experimental tradeoffs, image reconstruction, and data interpretation. Course will not be offered during Winter 2024 quarter; will resume in Winter 2025.

S. Riederer (Even: Winter) – A technical study of advanced topics in contemporary magnetic resonance imaging (MRI). Topics to be discussed include vascular imaging and flow assessment, motion effects and compensation, echo-planar imaging, parallel acquisition, cardiac imaging, and diffusion.

S. Riederer (Odd: Fall, Spring) – Seminar held weekly consisting of a presentation of some contemporary technical research topic in magnetic resonance.

L. Yu, S. Leng, C. McCollough (Even: Fall) – The objective of this course is to give students in-depth training in X-ray computed tomography, including analytical and iterative reconstruction; dose measurement, management and reduction; cardiac and multi-energy CT; current clinical applications; and emerging techniques. Hands-on lab work and programming will be required as part of this course.

K. Zhao (Approval Required) - This course incorporates advanced anatomy, kinematics, kinetics, and protocol development, with a focus on the student's specific research topic and interest. The course will culminate in a project that integrates the methods and applies them to a research question related to the student’s thesis work.

T. Meier (Winter) – This course provides instruction and hands-on experience in the use of common methods and techniques in physiology. It will acquaint students with regulations, information sources, and ethical considerations of responsible animal use in research. Lab directors will teach students techniques such as appropriate handling, sampling, anesthesia, and surgery of animal subjects, with an emphasis on rodents, including transgenic methods and rodent models.

K. Kaufman (Fall) – This course is an introduction to biomechanics laboratory methods, covering techniques spanning from the in-vitro tissue level to in-vivo joint biomechanics. The course will include hands-on experience in material testing, motion tracking, force measurement, EMG measurement, device accuracy testing, and data processing. Students will also become familiar with IRB and IACUC study requirements.

BMEP Faculty (Summer) – Review of contemporary topics in Biomedical Engineering literature to be arranged with individual BMEP faculty members. Prior approval from Program Director. Name of faculty with syllabus required for approval.

J. Miller (Approval Required) – Students will be exposed to advanced topics in cardiovascular physiology with an emphasis on Integrative control mechanisms in health and disease, structure and function, sex-based medicine and translational approaches to investigations. Students will be required to critically evaluate current literature, provide a historical overview of a specific topic and to write a review article on a topic of mutual interest to the group.

G. Sieck (Approval Required) – The goal of this course is to provide an in-depth account of the functional components of the respiratory system and their integration in health and disease.

Y. Prakash (Approval Required) – Students will be exposed to advanced topics related to smooth muscle signaling pathways, intracellular calcium regulation, pharmaco-mechanical coupling, etc.

M. Romero (Approval Required) – Renal hemodynamics, glomerular function, mechanisms and regulation of electrolyte transport.

A. Matveyenko (Approval Required) – This course will provide in depth understanding of key aspects of endocrine physiology in health and under conditions associated with various disease states. Students will be responsible for selecting a scientific topic related to endocrine physiology for detailed study. The course director will be responsible for assigning key research articles and other materials to facilitate student-centric learning process.

G. Sieck (Approval Required) – The goal of this course is to explore muscle physiology from the protein- protein interactions that establish the molecular basis of muscle contraction to the biomechanics of movement.

G. Sieck (Approval Required) – The goal of this course is to explore modeling and analysis of complex physiological systems: respiratory control, sleep apnea, and locomotion. A laboratory session and journal reviews are also planned to prove some of the above concepts and their applications.

G. Sieck, G. Worrell (Fall, Winter, Spring, Summer) – Course offered at the discretion of the instructors, or Fall term if the first option is not possible. This course is designed to explore the engineering applications in neuroscience. Included topics are the fundamental physical principles governing neural interface systems, relevant anatomy and physiology of the nervous system, and the conceptual design, optimization and implementation of neural interface technology. The course focuses mainly on neural interfaces and prosthetics.

G. Sieck, G. Worrell (Odd: Fall) – This course is designed to explore the engineering applications in neuroscience. Included topics are the fundamental physical principles governing neural interface systems, relevant anatomy and physiology of the nervous system, and the conceptual design, optimization and implementation of neural interface technology. This course focuses mainly on neural interfaces and prosthetics.

M. Romero (Fall) – In Systems Physiology I; The Cell as a Complex Biological System – the students will obtain a broader view of traditional “Cellular Physiology.” All systems are made up of components which must communicate and respond. This course will focus on the fundamental organization that exists at the molecular, cellular, tissue, organism and population levels.

TBA (Winter) – The course covers the modeling and analysis of the following complex physiological systems: Respiratory Control, Cardiac Dysrhythmias, Sleep Apnea, Neutrophil Density Regulation, Cardiovascular Variability, and Circadian Rhythms. Adaptive and nonlinear control concepts are explained and applied to these physiological systems, and where Matlab and Simulink are used for simulation. A laboratory session and journal reviews are also planned to prove some of the above concepts and their applications.

Margaux. B. Linde (Approval Required) – Lectures and discussions in physiology of both normal and abnormal bone. Classes are a combination of lectures and current topical literature. Topics will vary, depending on the interest of enrolled students.

TBD (Summer, Fall, Winter, Spring) - Independent studies are arranged on an individual basis in selected advanced topics in biomedical engineering and physiology. Learners are expected to define a topic area and parameters in consultation with a member of the teaching faculty and/or the program director. Specific assessments may vary but are required to demonstrate mastery of the topic. Independent studies are intended to emphasize laboratory/project-based learning (augmented with lecture/book content); this is in comparison to Tutorials which are intended to be primarily theoretical discussions on a topic (augmented with homework/labs). In addition to individual assignments for the course, students will be expected to submit a summary of their learning experience as a final assignment for review by the BMEP Curriculum Committee.