National Library of Medicine T-15 Training Grant
"A Systems Engineering Focus on Medical Informatics"

Overview of the Training Program Example Research Topics To Apply Program Faculty and Students Resources Available to Trainees

Overview of the Training Program

This program is designed to train a cadre of future researchers who are well-grounded in systems engineering research techniques and supported by expert faculty to augment the research, planning and quality assurance activities of the health system and to model and improve upon our understanding of biological systems.

Postdoctoral Fellowships. This medical informatics postdoctoral fellowship program is designed as:

1. a 2-year M.S. degree program tailored to biomedical informatics for those already holding a doctorate in the Nursing, Biological, Computing or Medical Sciences, or
2. a research-only fellowship program for those already holding a Ph.D. in Systems Engineering.

Prerequisites. Candidates should hold a doctoral degree in computer science, biology, nursing, medicine, systems engineering, or a similar degree. Specific prerequisites include multivariate calculus, linear algebra, differential equations, probability, statistics and computer programming. Candidates must be U.S. citizens or permanent residents.

Predoctoral Training. The predoctoral program is designed as a 5-year PhD beyond the B.S. or a 3-year PhD beyond the M.S. using the model of the current UVa Systems and Information Engineering PhD program tailored to healthcare infomatics. Trainees are given an annual stipend of $20,772-$39,772 (depending on previous degree and years of full-time work prior to enrolling), plus health insurance and a travel stipend. Tuition and fees are fully covered. Students are mentored by both a systems engineering faculty member and a healthcare faculty member.

Prerequisites. Candidates should hold a B.S. or M.S. in computer science, industrial and systems engineering or a similar field. Specific prerequisites include multivariate calculus, linear algebra, differential equations, probability, statistics and computer programming. Candidates must be U.S. citizens or permanent residents.

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Example Research Topics

Fellows will focus their research in healthcare information systems. Example research topics:

• Intelligent clinical user interfaces and decision support systems.
• Analysis and design of handoffs of care.
• The design, construction and testing of computerized and physical simulators for training clinical palpation and surgical skills.
• Use of mathematical and statistical approaches to aid in the evaluation and clinical interpretation of laboratory tests
• Analysis of medical longitudinal data using multivariate and nonlinear time series analysis
• Spatiotemporal analysis of medical images such as from MRI or digital x-rays
• Clinical laboratory automation, embedded sensors, and remote patient monitoring using the Internet and wide area communications.
• Consumer health informatics and evaluation of informatics tools and resources.
• The role of standards in support of data integration, data repositories, physician order entry, decision support, and the optimal use of clinical data for patient safety and clinical research.
• Design, structure, function, and utility of large patient data repositories for clinical and research purposes.
• Patient safety and the application of systems engineering techniques to prospectively study practices or retrospectively use chart review and data mining methods.
• Visualization of medical and biological data sets.

Students focus their Systems Engineering training in one of five areas of departmental expertise:

1. computational statistics and simulation
2. human-machine systems
3. optimization and control
4. risk and decision analysis
5. systems integration

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To Apply.
7-9 slots are available to start study in the summer or fall semester, 2007. Interested candidates should fill out the Department of Systems and Information Engineering pre-application form. However, official candidates must apply through the regular graduate engineering admission process for the Department of Systems and Information Engineering found at www.seas.virginia.edu/advising/admissions.php and should clearly indicate their desire to participate in this medical informatics training program in their essay. Applicants are strongly advised to contact one of the Systems and Information Engineering Professors on the Executive Committee (see list below) for more information prior to applying.

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Program Faculty
The program is administered by an 11-member Executive Committee:

• Stephanie Guerlain, Ph.D., Associate Professor, Systems and Information Engineering
• Jim Harrison, M.D., Ph.D. Associate Professor of Public Health Sciences and Pathology, Director of the Division of Clinical Informatics
• Peggy Plews-Ogan, M.D. Associate Professor of Internal Medicine
• Sarah Farrell, Ph.D., APRN, Associate Professor of Nursing and Public Health Sciences, Associate Dean for Academic Programs, School of Nursing
• Ellen Bass, Assistant Professor of Systems and Information Engineering
• Ginger Davis, Ph.D. Assistant Professor of Systems and Information Engineering
• Greg Gerling, Ph.D. Assistant Professor of Systems and Information Engineering
• Jason Lyman, M.D., M.S., Assistant Professor of Public Health Sciences
• Andrew Post, M.D., Ph.D., Assistant Professor of Public Health Sciences
• Wendy Cohn, Ph.D., Associate Professor of Public Health Sciences
• Gretchen Arnold, MLS, AHIP, Interim Director and Associate Dean, Claude Moore Health Sciences Library.

Advisory Board
The advisory board reviews the program quarterly

• Don E. Detmer, M.D., M.A. Professor of Medical Education at UVA and President and CEO of the American Medical Informatics Association (AMIA)
• Donald Brown, Professor and Chairman of the UVA SIE Department
• William Knaus, M.D., Professor and Chairman of Public Health Sciences
• Robert Reynolds, M.D., Professor and Acting Chair, Department of Public Health Sciences
• Stephen Borowitz, Professor of Pediatrics and Medical Director of the Clinical Information System, UVA Health System
• Jack W. Smith, M.D., Ph.D., Professor and Dean, University of Texas School of Health Information Sciences
• Paul Tang, M.D., Chief Medical Information Officer, Palo Alto Medical Foundation and Associate Clinical Professor, UCSF, Chair of AMIA.
• Richard I. Cook, M.D., Associate Professor of Anesthesiology and Director of the Cognitive Technologies Laboratory at the University of Chicago.

Program Students
The current students include:

Ph.D.:

• David Bauer
  
• Matthew Bolton
  
• Justin DeVoge
  
• Akilah Hugine
  
• Daine Lesniak
  
• Barbara Mooney
  
• Matthew Wagner

Postdoc:

• Kwangsik Nho

Short-term:

• Michael Paul Cary, Jr.

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Resources Available to Trainees

Academic Units

The University of Virginia (UVa) is a Carnegie I research institution comprising more than 20,000 students (over 13,000 undergraduates, approximately 4700 graduate students and 1700 professional students from all 50 states and nearly 100 countries) located in the city of Charlottesville. It has been ranked first or second among public research universities since US News & World Report began rankings in 1998, and is in the top 25 of all national research universities. It supports graduate and professional schools in Arts and Sciences, Architecture, Business, Commerce, Education, Engineering and Applied Science, Law, Medicine and Nursing, which are all collocated around the main university grounds. The University is known for a long tradition of collaboration and faculty development. While highly competitive for extramural support, within the institution there is a strong spirit of collaboration, mentoring and support of younger faculty and students, which creates a nurturing learning environment. Notably, the University also has a long history of leadership in academic ethics, with a student-managed Code of Honor that has been in effect for more than 150 years.

The School of Engineering and Applied Science (SEAS) is located on the main grounds of the University. It offers 9 undergraduate programs (more than 1900 students) and 31 graduate programs (more than 600 students) from 8 academic departments. The School received over $50 million in external funding for research and development in 2006.

The School of Medicine is part of the University of Virginia Health System, which is located adjacent to the University grounds and about a 15-minute walk from SEAS. It now has over 600 full-time faculty and 549 medical students. It is ranked 26^th in research among medical schools nationally (US News & World Report) and received over $133 million in NIH funding in 2006. The School of Medicine and Health System are in the midst of a 10-year strategic expansion plan that has seen the completion of two new research buildings and this year's groundbreaking for a new Cancer Center building.

The Health System is a major tertiary-care health sciences center serving a large geographic area surrounding central-west Virginia. The University Hospital includes 534 beds and a Level I trauma center, and Health System outpatient clinics are located adjacent to the Hospital and Medical School. The Health System supports over 541,000 outpatient visits, 57,000 emergency room visits and 27,000 inpatient admissions per year. A number of rural outreach programs, including a telemedicine program (see below) extend access to the Health System into rural environments.

The Department of Systems and Information Engineering is one of eight degree-granting departments in SEAS. It is collocated with all other schools and colleges on the University grounds, and is a 15 minute walk from the University Hospital. All SE predoctoral and postdoctoral trainees are provided office space, desktop computers and resources for copying, faxing, scanning, and printing. The department has a dedicated network manager and maintains its own wireless network and separate graduate and undergraduate computing labs for teaching and research. Departmental computers are equipped with software for modeling, statistics, software development and multimedia editing. Classrooms located in the department are equipped with computer and video projection. Twenty-five video-conferencing-enabled laptops are also available to support collaborative education.

The Department of Public Health Sciences in the School of Medicine was established in 1995 as the Department of Health Evaluation Sciences, under the leadership of William Knaus MD. The department is comprised of Divisions of Clinical Informatics, Biostatistics and Epidemiology, and Health Services Research, and was designed to be an innovative combination of disciplines supporting the measurement, management and analysis of health-related information. In 2005 the department added a Division of Public Health Policy and Practice and changed its name to Public Health Sciences. Currently, the department supports a Masters program in Public Health (MPH) and a 31-credit (1 year) MS degree in Health Evaluation Sciences with tracks in clinical research and clinical informatics. The department contains 35 faculty overall, with 17 support staff. The total external research funding for faculty was $2.9 million in 2005. There is a full-time network manager and seven servers (MS Windows, Linux and Mac OSX) supporting file services, statistical analysis, and software development and prototyping. The department is housed in approximately 10,200 sq. feet next to the Academic Computing in Health Sciences facility (see below) in the West Complex of the medical center. The West Complex is immediately adjacent to the main university grounds and connected with the University Hospital, Medical Library and medical research buildings by enclosed, raised walkways. In addition to faculty offices and staff workspaces, the departmental space contains a dedicated classroom seating up to 35 students with a projection monitor, computer with a network connection and audio equipment, screen and whiteboards. The departmental space, including the classroom, offers encrypted wireless Internet access. Notably, the Division of Clinical Informatics manages the Clinical Data Repository to support clinical research (see below).

Digital Library Initiatives at the University of Virgina Library reflect the vision of a distributed and flexible technology infrastructure that enhances access, manipulation, storage, distribution, and integration of information and services throughout the University of Virginia. This vision comes in part from the work of five committees that participated in the Library of Tomorrow (LofT) planning process in 2001, which developed a five-year program to transform the Library into the model university research library for the 21st century. Included initiatives include:

• FEDORA™ Version 2.1 available

• UVa Community Digitization Guidelines

• Digital Initiatives Terminology Glossary

• Highlighted Digital Collections Produced by the UVA Library

• UVa Library Participation in Digital Library Community Initiatives

Of special interest is the Fedora Project. Fedora version 2.1 was released on February 3, 2006. Fedora is a digital object repository management system upon which interoperable web-based digital libraries, institutional repositories, and other information management systems can be built.

The Claude Moore Health Sciences Library (Gretchen Arnold, Interim Director) is centrally located in the Health System facility and connected to the West Complex (Dept. of Public Health Sciences) and the medical research buildings by raised, enclosed walkways. The library subscribes to over 2300 journals in the basic and clinical sciences and contains over 80,000 monographs and 4400 multimedia programs. The library recently completed a major renovation that upgraded and expanded computer capabilities, increased the number of conference/small group teaching rooms and added a multimedia development laboratory. The library's systems are linked with institutional networks and provide online access to a variety of databases, many journals, and services such as Ovid, ScienceDirect, MDConsult, Web of Science, etc. The medical library also serves as a biomedical information resource for the University at large, the local community, and the Commonwealth through proactive outreach services, and the nation through cooperative programs with other libraries and agencies.

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Computing and Communications

The Office of Information Technologies and Communications (ITC) is the central resource for information technology leadership, academic and administrative support, network and communications infrastructure, and IT training, policy, planning and strategy for the University of Virginia. It is the home of over 260 professional and support staff and manages a yearly budget of approximately $30,000,000. ITC works closely with academic and administrative leadership and their respective units throughout the university to provide, maintain and constantly evolve a superb information technology environment for the various interrelated missions of the university.

The Academic Computing in Health Sciences (ACHS) facility is a joint venture between ITC and the Medical School Dean's Office formed twelve years ago to meet the academic computing needs of biomedical researchers. It is located in the West Complex of the medical center, immediately adjacent to the Department of Public Health Sciences. The client base includes approximately 500 faculty, staff and graduate students in over one hundred departments and centers. A staff of seven (plus a program support person) provides research-focused hardware and software support and training classes in an on-site computer classroom. The facility is accessible nights and weekends by registered users and nearly all services are free of charge. One area of concentration is providing image acquisition systems (ranging from high-magnification microscopes to large, high-resolution x-ray scanners), and training and consultation in the effective use of these systems. Users can acquire images (as well as videos, sound clips, etc.) and edit, process, or annotate them as needed to include in grant applications, presentations or publications. The second major area is in the design, creation, maintenance, and access of large databases. ACHS manages the hardware for the Clinical Data Repository (see below). It also maintains local copies of GenBank and UniPROT, performs several million searches per year using a large-memory Sun server and a 70-processor Apple Xserve cluster, and archives and publishes data acquired at the Biomolecular Research Facility core lab. It provides consultation to researchers who need to include a data management plan in their grant applications. Programming services are provided free of charge for "proof of concept" projects; for larger and/or longer-term projects, contract (for-fee) programming services are available. ACHS also works with the Department of Public Health Sciences and ITC's Research Computing Support Group to provide statistical consultation.

The University of Virginia network (UVaNet) has a 10 gigabit core with 1 gigabit connections to the majority of buildings on grounds. Connectivity within buildings to individual devices is generally 10/100 megabit but gigabit connections are routinely granted as needed for research and infrastructure services. UVa also has a parallel network that is protected by firewalls and VPNs for departmental desktops and servers, which is termed the More Secure Network (MSN). The MSN is currently 1 gigabit across the core with connectivity within a building set to 10/100/1000 as needed. Many university and medical center academic buildings are also served by a common encrypted wireless (802.11b) network for which authentication is carried out using university-provided digital certificates in combination with MAC address registration. The University supports several customized networks, such as the clinical portion of the Medical Center, which are developed for specific security needs and generally protect a small set of servers or a specific service. The customized networks are protected by firewalls and in a few cases with VPN technology. The rules of access and levels of security are customized for the services they protect. External connections to the Internet include two OC3 links and UVa is a member of the National LambdaRail Initiative, with a 10 gigabit connection that also handles traffic to Internet 2.

UVa offers several high performance computing clusters and support services for faculty and students. The university is also actively pursuing grid technology implementation on campus as well as regionally through the Southeastern Universities Research Association (SURA).

The University of Virginia's Health System Computing Services (HSCS) is directed by Barbara Baldwin, Health System CIO, and includes 130 staff members who are responsible for computer system planning, implementation, security, systems recovery, and customer support within the hospital and clinic environment. HSCS develops IT strategy for the Health System through customer and executive planning sessions and provides implementation and user support for IT systems in the healthcare setting. The current priorities include implementation and evolution of a physician- and patient-accessible electronic health record; empowering patients, employees and consumers through self-service Web portals; improving data management and reporting for quality and outcomes studies; IT support for optimizing organizational throughput and patient capacity; and increasing collaborative linkages among health care payers and providers.

The Health System has been a pioneer in the implementation of computerized physician order entry, which was initiated on the inpatient care units 20 years ago. It is now converting to the GE Healthcare clinical system and is an early adopter for GE clinical functionality. The Health System also has Kodak radiological and AGFA cardiology PACS as well as Streamline Health's document imaging. Laboratory and pathology data are managed with Misys Laboratory and CoPathPlus systems. These systems provide a contemporary electronic health care data management environment that supports critical analysis and process improvement. Health System Computing Services personnel have participated with students from SEAS in projects evaluating the scope and content of electronic medical records, evaluation of healthcare system throughput, and assessment of the impact of automation in ambulatory clinics.

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Specialized Facilities

The SIE Human-Computer Interaction Laboratory, managed by Drs. Guerlain, Bass and Gerling, is located in the Department of Systems and Information Engineering, and is equipped with 22 networked dual-monitor computer workstations along with analog and digital video capture, video editing workstations, video cameras and microphones, a control room, one-way mirror, all to support the design, evaluation and teaching of human-centered software development and conducting human-in-the-loop simulations with appropriate behavioral, task, and physiological data collection. The laboratory houses several locally developed specialized systems: the Eye Response Interface Computer Aid (known as ERICA), the Gazetracker software designed to track mouse, keyboard, and eye movement and record eye fixations and pupil diameter, and the RATE software developed to study and analyze distributed team behavior. The lab is also equipped with BioPac ®, a non-invasive technology used to record physiological responses and the SensAble Technologies PHANTOM Omni, an interactive device that simulates force-feedback to users making it possible for users to touch and manipulate virtual objects.

The University of Virginia Clinical Data Repository (CDR) is a large-scale integrated database containing clinical and administrative information on almost 900,000 patients and over 5 million clinical encounters¹. It was developed and is maintained by the Clinical Informatics Division of Public Health Sciences using open source and locally-developed software, and it represents the primary integrated data resource for clinical research and quality studies in the Health System. The CDR is under active development as it grows and changes to meet changes in data availability, patient privacy and security requirements, and research needs. We anticipate that the data in the CDR will be an important resource for students in the training program who investigate clinical care processes or outcomes, or carry out simulation and modeling studies. In addition, the development of the CDR itself will provide a fertile ground for projects related to modeling clinical data², designing and managing large clinical data sets for research use³, repurposing clinical data for education⁴ and communicating data between disparate systems.

The Teaching Resource Center
The Teaching Resource Center (TRC) at the University of Virginia is a center for collegial community and committed conversation about teaching and professional development issues at all levels and in all academic disciplines. The Teaching Resource Center promotes excellence in teaching and encourages intellectual connections throughout the University of Virginia in many ways, including these:

• Supports initiatives that value excellent teaching in a strong research institution
• Offers numerous programs and publications that highlight effective teaching and writing strategies, including workshops, confidential consultations, handbooks, and essays
• Creates opportunities for sharing expertise and wisdom about teaching, writing, and faculty growth
• Fosters and supports innovative teaching methods and technologies
• Cultivates conversations about academic writing and publishing
• Provides various services and consultations such as polling students as to perceptions on one's teaching, and videotaping and analysis of classroom teaching.

The TRC also offers numerous workshops each semester aimed at teaching and research career development for both faculty and graduate teaching assistants. Several recent topics include: Connecting Knowledge across Disciplines, Making the Most of Diversity, Grading with Rubrics, Tips on Writing Proposals to NSF, Manage Time and Get It Written, Secrets of Successful Academics, Learning to See Complexity: Teaching with Visuals in Text-based Disciplines, Reframing Diversity in Higher Education: An Exploration of Theoretical Paradigms, and Can We Talk? Methods and Principles for Interaction in a Lecture Setting. The TAs on this training grant will greatly benefit from these workshops and other TRC programs.

The University of Virginia Center for Quality and Patient Safety (CQPS) was developed in response to collaborations started in 1999 between the School of Medicine and Department of Systems and Information Engineering. The vision of this interdisciplinary Center was to bring together faculty from the School of Medicine with faculty from the Schools of Nursing, Law and Engineering to establish clinical best practices and carry out research and education in healthcare quality. The CQPS was officially introduced in 2005 and provides a forum for highlighting interdisciplinary research projects related to healthcare quality, such as some of the projects mentioned in the Collaboration section, and it provides a small grants program for startup projects. One of the goals of the CQPS is to create an environment in which quality questions generated in the clinical environment can stimulate critical interdisciplinary research, with results feeding back to improve clinical care. Several of the core faculty of CQPS (Plews-Ogan, Young, Guerlain, Voss, Schectman) are also core faculty of this training program proposal. We anticipate that the CQPS will develop into an important resource for the proposed training program, collaborating with both SE and CI/PHS in providing curriculum resources, research problems and mentors for our students.

The National Surgical Quality Improvement Program (NSQIP), of which UVA is a spearheading member, has patient history and symptomatic data from major general surgery and selected vascular patients prospectively coded and entered by experienced clinicians. This NSQIP database is consistent with the Veterans Administration coding of these data. Within just a few years, we expect to have access to well over one million cases, providing an exemplary opportunity for students interested in data mining.

The Clinical Performance Laboratory, directed by Dr. Jeffrey Young, occupies 550 sq. ft. on the third floor of the MR4 medical research building, adjacent to the University Hospital. The lab is designed for single- and multiple-subject clinical simulations and training sessions. It contains equipment for digital audio and video recording, and high performance audio playback. The lab is supported by a full-time lab assistant, who conducts the simulations, oversees recording, and performs transcriptions and analysis. The purchase of a computer controlled mannequin simulator is being considered for 2006. Since the lab opened, the lab has been used for six simulation studies, yielding four abstracts and several presentations. It was awarded a graduate medical education grant for 2005 and 2006.

The Laboratory for Clinical Learning (LCL) in the University of Virginia School of Nursing includes a clinical simulation lab designed to simulate clinical settings for teaching purposes. This is accomplished through the use of clinical case scenarios and resources that facilitate clinical critical thinking and decision-making. The clinical learning labs are located in four rooms on the third floor of McLeod Hall, on the Health System grounds and adjacent to the medical research buildings. The LCL includes the Theresa A. Thomas Intensive Care Simulation Laboratory, a state of the art facility equipped with human patient simulators and bedside computers with Internet access, digitalized video and computer assisted instructional software. The labs are designed to replicate realistic practice settings, including the basic hospital unit, critical care, pediatrics, neonatal nursery, maternity, health assessment and diagnostic laboratory. In March 2006, the School of Nursing sponsored a statewide Simulation Users' Group Conference, including about 100 representatives from academic institutions and health care systems, to help users of instructional simulations to better incorporate the technology into curricula and to share ideas to gain maximum educational benefit.

The University of Virginia Office of Telemedicine, directed by Dr. Karen Rheuben, provides remote diagnosis, consultation and patient care in all clinical specialties using video over links supporting H.320 (ISDN) and H.323 (video over IP) protocols to 60 sites in the University of Virginia Telemedicine Network and Southwest Virginia Alliance for Telemedicine. The Office was initiated in 1993 and has supported over 8000 patient encounters in rural sites and correctional facilities since then. It has received support from the US Departments of Commerce and Agriculture, the Virginia Department of Health, Anthem Blue Cross and Blue Shield, and other governmental and foundation sponsors. The video hub facility is centrally-located in the University Hospital and is supported by a 5-person staff.

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