Research Curriculum and Plan

Pulmonary and Critical Care Medicine Fellowship

Research Curriculum and Plan

All fellows in the Pulmonary and Critical Care Medicine (PCCM) fellowship training program are required to perform meaningful and tangible research. Fellows would be provided the proper tools to conduct research through a structured training program and would thereafter use the mentorship process and research project timeline in order to perform actual research under the guidance of a faculty mentor.


Research Training Program

Fellows in the Pulmonary and Critical Care Medicine fellowship will participate in a structured 15 days long training program in the first month (July) of their 2nd year of training.

The training program would consist of two parts:

  1. Introduction to Basic Science Research: supervised by Dr. Ruxana Sadikot
  2. Introduction to Clinical and Translational Research: Conducted by the CTSI

(Clinical and Translational Science Institute at UF)

  1. Description of the training program and Educational GoalsIn addition to the other research requirements of the fellowship, second-year fellows starting July of 2013 will be required to spend half a month in a basic research lab within the pulmonary and critical care medicine division in the mornings and participate in the CTSI conducted course in the afternoons. The goal of the training program is to give the fellow an introduction to the various facets of basic research, translational and clinical research which would be used as a platform to develop their research project over the subsequent 2 years. Another overall goal is to introduce the fellows to mechanistic, hypothesized-based research so that they can better understand the origins of research discovery as it relates to translational science and medicine. Ultimately, the experience will provide a greater understanding and appreciation for basic and translational science and the fundamental role that it plays in medicine today.  To meet the research requirements of the fellowship, the fellow may continue their research project started during this training or to select a clinical project under the mentorship of one of the clinical faculty.
  2. Educational Objectives:The following are the educational objectives and experiences for the research training:

Basic Science:

  • Learn basic laboratory skills and techniques.
  • Understand protein expression techniques — measure protein content of tissue extracts and then perform western blotting
  • Understand gene expression techniques — isolate and quantify mRNA, create cDNA, and perform reverse transcription PCR
  • Learn necropsy techniques in animal models
  • Learn a metabolic assay in tissue or cell culture
  • Monitor a basic science technique occurring in human subjects
  • Present at least one article related to an advanced technique during these two weeks within the group

Clinical and Translational Science:

  • Understand how to develop a research question
  • Understand the kinds of and how to develop a study design
  • Understand the Institutional Review Board (IRB) applications process
  • Understand the concept behind and usage of relational databases
  • Understand the basics of research statistics
  • Recognize the local resources available for research
  • Develop a mock project in the ‘Small Groups’ workshops

III. Organization of the Research Training Program:

The research training program will be held in the second half of July each year. The first half of the day will be dedicated to basic science research training. Early morning didactic sessions would be followed by hands-on practical training in the laboratory. This research experience will be supervised and monitored by Dr. Ruxana Sadikot. The afternoons will be dedicated to the “Introduction to Clinical and Translational Research” course provided by the CTSI. A sample structure of these two is as below:

Introduction to Basic Science Research

Lecture Series ( 8:00 AM to 9:00 AM Day 1 to Day 11)

1) Approach to Hypothesis Driven research and Developing Specific Aims – RT Sadikot

2) Basics of Molecular Biology – ML Brantly

3) Protein – L Moldawer

4) RNA – K Mohammad

5) DNA – N Kamal

6) Genomics and Proteomics – ML Brantly

7) Cell Studies Basics – Jorge Lascano

8) Animal Models For Human Diseases – M Mohammadzadeh

9) Bench to Bedside- How to apply basic studies to human diseases – RT Sadikot

10) Analysis of Data in a lab – G wang

11) Molecular Biology Journal Club – Jorge Lascano

Practicum (9:00 AM to 12:00 PM):

Basic Laboratory Skills – R Roman

Cell Culture – Jorge Lascano

Protein – Z Yuan

RNA – R Roman

DNA – R Roman

Animal Studies – Z Yuan

GMS 7093: Introduction to Clinical/Translational Research

Day 1: Ideas to Hypotheses: Examples of Clinical/Translational Research Moderator: Ronald Shorr, MD, MS

2:00-2:30 PM Ron Shorr – Course overview

2:30-3:00 PM Linda Cottler – How and why I do community based research

3:00-3:30 PM Elizabeth Shenkman – How and why I do outcomes research

3:30-4:00 PM Debbie Treise – How and why I do qualitative research

4:00-4:30 PM Jon Shuster – Small group intro

4:30-5:00 Small group assignments

Day 2: Developing the Research Question Moderator: Jon Shuster, PhD

2:00-2:30 PM Jennifer Lyon – Has it been done before?

2:30-3:00 PM Ron Shorr – Are the data available? Secondary data analysis

3:00-3:30 PM Jon Shuster – Is it feasible?

3:30-4:00 PM Mark Segal – Framing aims

4:00-5:00 Small Groups

Day 3: Study Design Moderator: Wayne McCormack, PhD

2:00-3:00 PM J. Glenn Morris – Overview of observational and interventional studies

3:00-4:00 PM Mini Devidas – Evaluation of clinical trials

4:00-5:00 Small Groups

Day 4: Data Management Tools Moderator: Douglas Theriaque

2:00-2:40 PM Douglas Theriaque – Data management issues and principles

2:40-3:30 PM Christopher Barnes – How to make a data management plan

3:30-4:00 PM Douglas Theriaque – Introduction to REDCap

4:00-5:00 Small Groups

Day 5: Statistical Considerations Moderator: Ron Shorr

2:00-2:15 PM Ron Shorr – Why learn statistics?

2:15-3:15 PM Cyndi Garvan/Under the hood of research Ron Shorr

3:15 AM-3:45 PM Cyndi Garvan/ Statistical software considerations Ron Shorr

3:45-4:00 PM Yueh-Yun Chi – How to learn statistics at UF

4:00-5:00 Small Groups

Day 6: Local Resources: CTSI Moderator: Jon Shuster

2:00-2:20 PM Mike Conlon – Intro to the Clinical and

Translational Science Institute

2:20-4:00 PM Jon Shuster – Research Design and Analysis Program (RDAP)

4:00-5:00 Small Groups

Day 7: Local Resources: Continued Moderator: Eve Johnson, MA

2:00-2:30 PM Jennifer Lyon – Library and reference resources

2:30-3:00 PM Teresa D’Angelo – UF Clinical Research Center (CRC)

3:00-4:00 PM Felix Liu – Integrated Data Repository

4:00-5:00 Small Groups

Day 8: IRB and Regulatory Considerations Moderator: Wayne McCormack

2:00-2:30 PM Tiffany Pineda – Overview of the IRB

2:30-3:15 PM Ray Moseley – Ethical and patient considerations

3:15-3:45 PM Everall Peele – HIPAA

3:45-4:00 PM Edythe Zettler – Research billing compliance

4:00-5:00 Small Groups

Day 9: Other Issues and Opportunities Moderator: Eve Johnson

2:00-2:30 PM Gary Wimsett – Conflict of interest policy and procedures

2:30-3:15 PM Wajeeh Bajwa – Investigational New Drug (IND) applications

3:15-4:00 PM Taimour Langaee – Genetics and Pharmacogenetics resources

4:00-5:00 Small Groups

Day 10: Career Development Awards: Next Steps Moderator: Ron Shorr

2:00-2:30 PM Susan Nayfield – NIH grants

2:30-3:00 PM Scott Berceli – VA grants

3:00-3:30 PM Rhonda Cooper-Dehoff Success story: NIH K23

3:30-4:00 PM Mark Brantly – Mileposts and guidelines

4:00-5:00 Small Groups

Day 11: Small Group Presentations Moderator: Marian Limacher, MD

  1. Competency-Based Objectives:

Medical Science Knowledge

Goal: Fellows are expected to learn clinical and translational as well as basic laboratory skills and to understand the various techniques utilized in basic medical science laboratories today.

Objectives & Competencies:

  1. Demonstrate basic science skills.
  2. Demonstrate understanding of the basic science techniques in the practicum part of the training.
  3. Demonstrate understanding of the clinical and translational research skills in the small groups workshop

Practice-Based Learning and Improvement

Goal: Fellows should demonstrate the ability to investigate and evaluate the project they are assigned, and to appraise and assimilate scientific evidence.

Objectives & Competencies:

  1. Identify strengths, deficiencies and limits in one’s knowledge and expertise, set learning goals, and identify and perform appropriate learning activities.
  2. Incorporate formative evaluation feedback into daily activities.
  3. Locate, appraise and assimilate evidence from published scientific studies related to their research project.
  4. Use information technology to optimize learning.
  5. Make one journal club presentation during the training program.

Interpersonal and Communication Skills

Goals: Fellows must demonstrate interpersonal and communication skills that result in the effective exchange of information and collaboration with the fellow’s mentor, other team members, and with other participants in the training program.

Objectives & Competencies:

  1. Communicate effectively with the fellow’s research mentor and members of the research team.
  2. Work effectively as a member of a research team.
  3. Maintain accurate, appropriate, timely and legible records.


Goal: Fellows must demonstrate a commitment to carrying out professional responsibilities and an adherence to ethical principles.

Objectives & Competencies:

  1. Exemplify integrity and respect for others.
  2. Demonstrate a good attitude.
  3. Demonstrate the ability to function as an effective member of a basic science team.
  4. Show up for duties on time and perform all needed work.
  5. Demonstrate a commitment to learning.
  6. Methods of Evaluation: Ongoing feedback is given to the research trainee by the faculty throughout the training program. Attendance will be kept for both parts of the training program. 80% or higher attendance will be required for successful completion of the training program. From a basic science training perspective at the end of the series, Dr. Ruxana Sadikot will approve that the fellow spent sufficient time in the laboratory, learned the expected techniques, and took part in seminars and journal clubs to an adequate level. A formal written evaluation will be completed and submitted to the fellowship program director. CTSI will monitor the participation of the fellows in the Clinical and Translational Research course and upon successful completion the fellows will receive a certificate of completion.