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Physiological Systems I

BME 5000 - Physiological Systems I

Eleven major human organ systems are covered in this course, including: integumentary, endocrine, lymphatic, digestive, urinary, reproductive, circulatory, respiratory, nervous, skeletal, and muscular.

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BME 5010 - Research Methods in Biomedical Engineering

An inquiry into the nature of research with emphasis on the spirit, logic, and components of the scientific methods. Health related research literature is used to aid the student in learning to read, understand, and critically analyze published materials. The preparation of research proposals and reports is emphasized. (Also offered as GPAH 6306.)

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BME 5020 - Clinical Engineering Fundamentals

Provides the fundamental concepts involved in managing medical technology, establishing and operating a clinical engineering department, and the role of the clinical engineering designing facilities used in patient care. Topics covered include managing safety programs, technology assessment, technology acquisition, the design of clinical facilities, personnel management, budgeting and ethical issues of concern to the clinical engineer.

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BME 5030 - Human Error and Medical Device Accidents

This course teaches the basic principles needed to analyze medical devices, medical device users, medical device environments and medical device accidents. It particularly focuses on human factors engineering as an important step to minimizing human error. The role of medical device manufacturers, medical device regulators and medical device owners will be examined to identify their role in reducing medical device use errors and medical device accidents. The nature and types of human error as well as a taxonomy of medical device accidents will also be presented. Investigative techniques involving root cause analysis and failure modes and effects analysis will be taught and applied to industrial and medical device accidents. Operating room fires, electrosurgical and laser burns, anesthesia injuries, infusion device accidents, catheters and electrode failures and tissue injury in the medical environment will be discussed in detail. A semester project will require the student to employ these tools and techniques to analyze a medical device accident.

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BME 5040 - Medical Instrumentation in the Hospital

This course will examine 10-12 current major technologies in use by healthcare practitioners. It will review the physiological principles behind each technology, the principles of operation, major features, methods for testing and evaluating each technology and will highlight available versions of the devices on the market today. Technologies to be covered will be selected from anesthesia equipment, surgical and ophthalmic lasers, cardiac assist devices, surgical & endoscopic video systems, radiographic and fluoroscopic devices, CT, MRI, ultrasound imaging equipment, radiation therapy, nuclear medicine, clinical chemistry analyzers, spectrophotometers and hematology analyzers. The course will be based on one text, selected manufacturers training documents as well as journal articles from current medical publications. Grading will be based on exams, quizzes, a semester project and class participation. Several classes will take place on site in Hartford area hospitals in order to observe and examine the equipment being discussed.

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BME 5050 - Engineering Problems in the Hospital

This course will cover engineering solutions to problems that are found in the healthcare environment. This includes a wide variety of topics such as electrical power quality of and the reliable operation of high tech medical equipment; electrical safety in the patient care environment; electromagnetic compatibility of various medical devices and electromagnetic interference; radiation shielding and radiation protection; medical gas systems, medical ventilation systems and indoor air quality; fire protection systems required in the hospital; networking medical devices, patient information systems, digital imaging and image storage systems; telemedicine and medical image transmission; and finally, hospital architecture and the design of patient care facilities.

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BME 5060 - Clinical Engineering Rotations I

This course is associated with the clinical engineering rotations that interns experience in hospitals, such as surgeries, CT, MRI, ICU, clinical laboratory and physical therapy.

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BME 5061 - Clinical Engineering Rotations II

This course is associated with the clinical engineering rotations that interns experience in hospitals, such as surgeries, CT, MRI, ICU, clinical laboratory and physical therapy.

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BME 5070 - Clinical Systems Engineering

This course primarily covers medical device connectivity and interoperability. This includes connecting medical devices to the hospital computer network to pass data to the patient medical record or to other medical devices for the purpose of feedback and control. The course will cover basic networking concepts, hospital network architecture, medical systems security and risk management, the role of interconnecting middleware, HL7 and DICOM data standards, moving data on the network, clinical information systems, digital imaging and image storage systems, medical device plug-and-play concepts, and a medical device integration project walk-thru.

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BME 5099 - Independent Study

Individual exploration of special topics as arranged by the student with an instructor of his or her choice.

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BME 5100 - Physiological Modeling

Unified study of engineering techniques and basic principles in modeling physiological systems. Focuses on membrane biophysics, biological modeling, and systems control theory. Significant engineering and software design is incorporated in homework assignments using MATLAB and SIMULINK. Recommended preparation: BME 211 and BME 251 (or equivalent).

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BME 5150 - Dynamical Modeling of Biochemical Networks

Recent advances in biological measurement technology have opened up a new era in quantitative biology. Part of this revolution is the new field of systems biology, which consists of viewing processes in biological cells as a whole, rather than considering one gene or protein at a time. Systems biology relies heavily on mathematical models of cellular processes, often derived from the microscopic laws of chemical and enzyme kinetics. In this course we will focus primarily on continuum (differential equation) models of cellular processes arising from these microscopic laws. Because most of these models wind up being nonlinear, we will spend a lot of time learning techniques to analyze systems of nonlinear ordinary differential equations, and we will explore the fundamental differences between linear and nonlinear systems. Biological applications will include modeling observed error rates in protein translation, using system nonlinearities to design biological toggle switches, and exploring biological motifs that lead to oscillations, switches, and other behaviors.

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BME 5210 - Biomedical Optics: Tissue Optics, Instruments and Imaging

Principles and imaging of biomedical optics. Optical absorption, scattering and their biological origins, radiative transfer equation and diffusion theory, diffuse optical tomography, Monte Carlo modeling and photon transport in biological tissue, ballistic light imaging, time domain, frequency domain and continuous light measurement systems, optical coherence tomography, and photoacoustic tomography.

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BME 5302 - Biochemical Engineering for Biomedical Engineers

Introduction to chemical reaction kinetics; enzyme and fermentation technology; microbiology, biochemistry, and cellular concepts; biomass production; organ analysis; viral dynamics.

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BME 5329 - Advanced Ultrasonic Imaging Techniques

Introduction to advanced techniques of ultrasonic image formation for biomedical applications. Introduction to acoustic wave propagation. A, B, C, M and Doppler ultrasonic imaging modes. Interaction of ultrasound with biological tissue. Acoustical holography. Ultrasonic transducer design and calibration. Transducer arrays. Ultrasound detection modes. Laboratory demonstrations will include Schieren visualization of ultrasound fields and transducer calibration techniques. Assumes a background in linear systems.

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BME 5339 - Introductory Ergonomics for Biomedical Scientists and Engineers

This problem-based course begins with a work-related overview of the design strengths and limitations of human anatomy and physiology (molecular, tissue and systems levels) and the contribution of work/worker mismatches to the development of disease. Measurement of the response of these biological tissues and systems to work-related stressors is examined, to define the mechanism and presentation of musculoskeletal disorders. The course addresses physiological and anatomical damage due to biomechanical, psychosocial and work organization stressors and explores the range of possible control strategies of interest to the engineer and public health practitioner. To measure presence and levels of risk factors, students will be introduced to the use of laboratory techniques (e.g., EMG, digital motion capture, force cells) as well as field methods used in ergonomic work-site assessment, ranging from simple check-lists (geared towards worker-based interventions), through detailed time/motion studies, self-report effort scales, epidemiological instruments, and psychosocial and organizational measurement tools. A research project is required.

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BME 5341 - Exposure Assessment in Ergonomics

The goal of the course is to develop a broad understanding of ergonomic risk factors, knowledge of the measurement modalities available for characterizing workplace risk, and an appreciation of the advantages and disadvantages of each modality. Students will be introduced to the use of laboratory techniques (EMG, videotaping and digitization, digital motion capture, force cells, accelerometry and exercise physiology). They will also be instructed in methods used in ergonomic work-site assessment, ranging from simple check-lists (geared towards worker-based interventions), through detailed time/motion studies, self-report effort scales, epidemiological instruments, and psychosocial and organizational measurement tools. The grade will depend on completion of a laboratory-based, field or epidemiological project.

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BME 5500 - Clinical Instrumentation Systems

Analysis and design of transducers and signal processors; measurements of physical, chemical, biological, and physiological variables; special purpose medical instruments, systems design, storage and display, grounding, noise, and electrical safety. These concepts are considered in developing devices used in a clinical or biological environment. Recommended preparation: ECE 210W, BME 251, and 252 (or equivalent).

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BME 5600 - Human Biomechanics

Applies principles of engineering mechanics in the examination of human physiological subsystems such as the musculoskeletal system and the cardiovascular system. Topics drawn for biosolid mechanics, biofluids, and biodynamics, the viscoelastic modeling of muscle and bone, non-Newtonian fluid rheology, blood flow dynamics, respiratory mechanics, biomechanics of normal and impaired gait, and sport biomechanics.

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BME 5700 - Biomaterials and Tissue Engineering

A broad introduction to the field of biomaterials and tissue engineering. Presents basic principles of biological, medical, and material science as applied to implantable medical devices, drug delivery systems and artificial organs. Also offered as MEDS 5313.

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BME 5800 - Bioinformatics

Advanced mathematical models and computational techniques in bioinformatics. Topics covered include genome mapping and sequencing, sequence alignment, database search, gene prediction, genome rearrangements, phylogenetic trees, and computational proteomics. Recommended preparation: BME 280 (or equivalent).

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BME 6020 - Physiological Systems II

A problem based learning course that focuses on in-depth coverage of four human organ systems. Format: didactic session followed by group problem solving. Also offered as MEDS 6472.

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BME 6086 - Special Topics In Biomedical Engineering

Classroom and/or laboratory courses in special topics as announced in advance for each semester.

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BME 6094 - BME Graduate Seminar

Presentations will be given by invited speakers from outside, faculty members, and student presenters on current research topics in biomedical engineering.

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BME 6110 - Computational Neuroscience

Explores the function of single neurons and neural systems by the use of simulations on a computer. Combines lectures and classroom discussions with conducting computer simulations. The simulations include exercises and a term project.

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BME 6120 - Neuronal Information Processing and Senory Coding

Processing, transmission, and storage of information in the central and peripheral nervous systems. Mechanisms of signal generation, transmission and coding by neurons and dendrites. Analysis of invertebrate and vertebrate visual and auditory systems, including: mechanisms of neurosensory transduction, coding, and signal-to-noise ratio enhancement. Neural spatio-temporal filters for feature extraction and pattern recognition. Information theoretic analysis of signal encoding and transmission in the nervous system. This course assumes a background in linear systems and feedback control systems.

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BME 6125 - Digital Image Processing

Problems and applications in digital image processing, two-dimensional linear systems, shift invariance, 2-D Fourier transform analysis, matrix Theory, randomimages and fields, 2-D mean square estimation, optical imaging systems, image sampling and quantization, image transforms, DFT, FFT, image enhancement,two-dimensional spatial filtering, image restoration, image recognition, correlation, and statistical filters for image detection, nonlinear image processing, and feature extraction. Also offered as ECE 6125

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BME 6126 - Optics for Biomedical Engineers

Learning optical imaging fundamentals. Topics include: review of two-dimensional linear system theory; scalar diffraction theory, wave optics, Fresnel and Fraunhofer diffraction; imaging properties of lenses; image formation; optical resolution in imaging, frequency analysis of optical imaging systems; imaging with coherent and incoherent light sources, coherent transfer function; optical transfer function, point spread function, fundamentals of microscopy, two-dimensional spatial filtering; coherent optical information processing; frequency-domain spatial filter synthesis; holography. Also offered as ECE 6126.

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BME 6130 - Systems Identification of Physiological Systems

Overview of linear and nonlinear methods for determining the input-output relationship of sensory and other physiological systems. Topics include: white noise analysis using the Voltera and Wiener expansion of non-linear system, moving average and autoregressive models, transfer function method, parametric identification using least-squares method, multi-input systems, spectrotemporal and spatiotemporal reverse correlation, spectral estimation methods using coherence. Examples from a host of neuronal systems will be provided, including the mammalian and amphibian visual and auditory systems

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BME 6140 - Cellular Systems Modeling

Cellular response to drugs and toxins, as well as normal cell processes such as proliferation, growth and motility often involve receptor-ligand binding and subsequent intracellular processes. Focuses on mathematical formulation of equations for key cellular events including binding of ligands with receptors on the cell surface, trafficking of the receptor-ligand complex within the cell and cell signaling by second messengers. Background material in molecular biology, cell physiology, estimation of parameters needed for the model equations from published literature and solution of the equations using available computer programs are included. Examples from the current literature of cell processes such as response to drugs and proliferation will be simulated with the model equations.

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BME 6143 - Image Recognition

Review of probability and stochastic processes. Statistical pattern recognition. Nonlinear signal processing and feature extraction. Correlation filters. Metrics for pattern recognition. Baysian classifiers. Minimum probability of error processors. Supervised and unsupervised learning. Perception learning methods. Multilayer neural networks. Applications to security and encryption. Also offered as ECE 6143

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BME 6150 - Computational Cell Biology for Biomedical Engineers

In the last decade, interdisciplinary science has established itself as a leading area of scientific investigation. The use of physics and mathematics to help understand biological systems hints at being one of the major scientific frontiers of this coming century. This course looks at biology at three separate length scales: molecular, cellular, and organismal/population. We will find that the math/physics of elasticity, hydrodynamics, statistical mechanics and reaction/diffusion can explain a broad range of phenomena throughout these size ranges. This course stresses the physical intuition of how to apply quantitative methods to the study of biology through the use of dimensional analysis, analytic calculation and computer modeling.

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BME 6160 - Computational Genomics

Advanced computational methods for genomic data analysis. Topics covered include motif finding, gene expression analysis, regulatory network inference, comparative genomics, genomic sequence variation and linkage analysis.

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BME 6180 - Computational Foundations of Systems Biology

The use of computers has become critical in many fields of science and engineering. In this course students will be introduced to computational systems biology which focuses on studying dynamic and intelligent features (e.g., adaptation and robustness) of biological systems such as gene networks. It will be emphasized the tools and methods of computational systems biology come from other computation-oriented fields such as computational physics, digital signal processing, control engineering, and digital logic. Students will also learn skills in programming using MATLAB, LabVIEW, and C# in the context of modeling, analyzing, estimating, and controlling real biological systems. Through a variety of assignments and projects, students will obtain a deeper understanding of physical and engineering principles applied to biological systems. Students will also read and present journal articles on topics covered in class, which will expose them to interdisciplinary research and views. This course cannot be taken for credit if students already took BME 4985.

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BME 6400 - Biomedical Imaging

Fundamentals of detection, processing and display associated with imaging in medicine and biology. Topics include conventional and Fourier optics, optical and acoustic holography, thermography, isotope scans, and radiology. Laboratory demonstrations will include holography and optical image processing. Assumes a background in linear systems. Recommended preparation: BME 251 or ECE 232 (or equivalent).

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BME 6420 - Medical Imaging Systems

This course covers imaging principles and systems of x-ray, ultrasound, optical tomography, magnetic resonance imaging, positron emission tomography.

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BME 6450 - Optical Microscopy and Bio-imaging

The course presents the current state of the art of optical imaging techniques and their applications in biomedical research. The course materials cover both traditional microscopies (DIC, fluorescence etc.) that have been an integrated part of biologists’ tool-box, as well as more advance topics, such as single-molecule imaging and laser tweezers. Four lab sessions are incorporated in the classes to help students to gain some hand-on experiences. Strong emphasis will be given on current research and experimental design. Also offered as MEDS 6450.

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BME 6460 - Advanced Optical Microscopy and Bio-imaging

This course will cover several aspects of state of the art biological and biophysical imaging. We will focus on advanced techniques including nonlinear optical processes (multi-photon excitation, second harmonic generation, and stimulated Raman processes), as well as optical coherence tomography. 3 lab projects will supplement the lectures, providing hands-on experience with nonlinear optical methods. Special emphasis will be given to current imaging literature and experimental design. Also offered as MEDS 6460.

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BME 6500 - Biomedical Instrumentation I

Origins of bioelectric signals; analysis and design of electrodes and low noise preamplifiers used in their measurement. Statistical techniques applied to the detection and processing of biological signals in noise, including the treatment of nerve impulse sequences as stochastic point processes. Methods of identifying the dynamic proper ties of biosystems. Assumes a background in linear systems and electronics.

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BME 6510 - Biomedical Instrumentation Laboratory

Experimental investigation of electrodes, transducers, electronic circuits and instrumentation systems used in biomedical research and clinical medicine.

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BME 6520 - Biosensors

Principles and design of acoustic imaging transducers, and force, pressure and hearing sensors. Covers also optical biosensors including oxygen monitoring sensors, glucose sensors and optical sensors used in imaging.

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BME 6610 - Biofluid Mechanics

Provides a foundation for continued studies of biofluid mechanical subjects. Topics covered include kinematic principles, the Navier-Stokes equations, the vorticity equation, unsteady fluid flows of physiologic relevance, turbulence and interfacial phenomena. Emphasis is placed on physical analysis of the cardiovascular and pulmonary systems, as well as of other biologic systems of interest.

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BME 6620 - Biosolid Mechanics

Mechanical behavior of biological solids. Applications of the theories of elasticity, viscoelasticity, and poroelasticity to bones, ligaments and tendons, skeletal muscle, and articular cartilage. Axial, bending, shearing and torsional loadings. Bone morphology and growth. Biphasic theory. Failure theories. Research paper. Topics may be modified slightly to accommodate student interests. Recommended preparation: BME 261, CE 287, and BME 312 (or equivalent).

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BME 6630 - Biodynamics

Dynamic modeling of biological systems using three-dimensional rigid body dynamics with a review of kinematics and kinetics and three-dimensional vector calculus. Applications of Newtons Laws and Lagrangian Equations presented. A critical review of various biodynamic assessment techniques and the principles of their operation will also be discussed. Biodynamic data analysis techniques will be shown along with fundamental model construction.

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