Level 1 Course Schedule MECOR Turkey 2015

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1 American Thoracic Society Turkish Thoracic Society Level 1 Course Schedule MECOR Turkey 2015 (Methods in Epidemiologic, Clinical & Operations Research) Cesme, Turkey November 2-7, 2015

ACKNOWLEDGMENTS The American Thoracic Society is the primary sponsor of the 2015 MECOR Turkey Course in Cesme, Turkey The Turkish Thoracic Society has provided the principle support for MECOR Turkey

2 ACKNOWLEDGMENTS The American Thoracic Society is the primary sponsor of the 2015 MECOR Turkey Course in Cesme, Turkey The Turkish Thoracic Society has provided the principle support for MECOR Turkey Our sincere thanks to all who have shared the vision and support this program The American Thoracic Society acknowledges and gratefully thanks Füsun Eyüboğlu, country coordinator of MECOR Turkey 2015 and her colleagues who assisted in its organization. MECOR Turkey 2015 Course Staff A. Sonia Buist, ATS MECOR Program Director Füsun Eyüboğlu, MECOR Turkey Country Course Director Fran Du Melle, Sr. Director, International Activities, American Thoracic Society Improving global lung health through development of local, country and regional lung disease research capacity 2

3 TABLE OF CONTENTS Acknowledgements... i Welcome... 1 Course Overview... 1 Expectations Resources... 1 Text Helpful Websites Other Helpful Resources Faculty... 3 Competencies... 6 Protocol Outline... 8 FINER Criteria x 2 Table Format Course Schedule

4 WELCOME TO MECOR TURKEY 2015! Congratulations and welcome to the MECOR family. In the next week you ll deepen your understanding of research epidemiology and establish new friendships with others in your field. We ll begin by introducing all MECOR faculty and participants in Monday morning s plenary session. Come prepared to introduce yourself, including your degree, institution and area of research interest. Please review this syllabus before the course begins. We will address any questions you have in the first session. COURSE OVERVIEW The main focus of Level 1 is to learn how to develop a study protocol. Students will learn the fundamentals of posing a testable research question, the various study design options for generating and testing hypotheses, and basic analytic skills. Students will spend time in lectures or working in small groups with or without a faculty member. By the end of the week, each student should have a research study protocol and PowerPoint summary to be used in a final presentation to MECOR faculty and students. Expectations We expect all participants in MECOR Turkey Level 1 to: Participate fully in all course activities, including daily check-ins, lectures and small group work; Read relevant sections of the textbook (see below); Seek help from Level 1 or other faculty when they encounter problems or need to review their plans/progress; and, Fully engage in preparing and presenting their research protocol. To enable you to meet these expectations, the faculty will be available during breaks and meals as well as after class. Please feel free to make appointments to meet with us. We welcome the opportunity to discuss your research interests with you. NOTE: Each Level 1 MECOR student is expected to bring his/her own laptop to the course. No computers or laptops will be provided. Nor will it be possible for students to share laptops since each person will be working concurrently on their own study. RESOURCES Textbook The MECOR course textbook for all levels is: Hulley SB, et al. Designing clinical research: an epidemiologic approach. 4 th edition. Philadelphia: Lippincott Williams & Wilkins, Please bring this text to the course. Note: The earlier (3 rd ) edition is perfectly suitable and is available used at lesser cost. 1

5 Helpful Websites Statistics at Square One (British Medical Journal): This is an excellent review of basic medical statistics. Southwest Oncology Group for clinical trials: This site is primarily designed for clinical trials work but can be used for other analyses. Designs covered include onesample and two-sample binomial, normal and survival calculations, plus two-stage clinical trials designs. Does not cover regression models. Logistic regression works only for one dichotomous predictor (via two-sample binomial). Note that it also has some simple statistical calculations (2x2 tables) and probability calculations (binomial, normal). UCLA: UCLA s statistical calculators run JAVA applets to estimate sample size needs for two-sample Poisson, ANOVA, Fisher s exact test, correlation/regression, t-test with unequal variances, nonparametric rank sum and sign tests, and other features. Dartmouth-Hitchcock Norris Cotton Cancer Center: This site does logistic regression with a continuous exposure variable and one additional continuous covariate or confounder. Vanderbilt University: This site is posted by Vanderbilt s CTSC group, which has developed a downloadable free program for Power and Sample Size calculation. University of Iowa: Russ Length s excellent website covers many ANOVA and regression designs, repeated measures, and a lot more. This is a superb resource with the ability to work out power for contrasts, generate power curves, and so on. Other Helpful Resources 1. Gordis L. Epidemiology. Third edition. Elsevier Saunders, Philadelphia, PA Glantz, Stanton A. Primer of biostatistics / Stanton A. Glantz. 6th ed. New York: McGraw-Hill Medical Pub. Division, IUATLD Monograph: Research Methods for the Promotion of Lung Health, A Guide to Protocol Development for Low-Income Countries." You will find this at the International Union against Tuberculosis and Lung Disease web site at: 2

LEVEL 1 FACULTY Tricia LeVan, PhD, CPH Associate Professor University of Nebraska Medical Center 985910 Nebraska Medical Center Omaha, NE 68198-5910 Telephone: 402-559-3985 tlevan@unmc.edu Dr.

She is Molecular Biologist and Genetic Epidemiologist with a research emphasis on genetic, epigenetic and environmental influences of chronic obstructive pulmonary disease (COPD).

6 LEVEL 1 FACULTY Tricia LeVan, PhD, CPH Associate Professor University of Nebraska Medical Center Nebraska Medical Center Omaha, NE Telephone: tlevan@unmc.edu Dr. LeVan is an Associate Professor in the Division of Pulmonary, Critical Care, Sleep and Allergy and the Department of Epidemiology. She is Molecular Biologist and Genetic Epidemiologist with a research emphasis on genetic, epigenetic and environmental influences of chronic obstructive pulmonary disease (COPD). Her research focuses on susceptibility genes that modulate lung innate immune response to acute and chronic exposure to bacteria, using organic dust from the agricultural environment as a model system. She currently teaches an Introduction to Epidemiology core course and a Genetic Epidemiology course for Certificate, MPH and PhD graduate students in the College of Public Health. She has been teaching MECOR courses since 2011 including courses in China, India, and Turkey. Sonia Buist, MD Pulmonary and Critical Care Medicine Oregon Health & Science University 3181 SW Sam Jackson Park Road Portland, OR buists@ohsu.edu Dr. Sonia Buist is currently Professor Emerita of Medicine at the Oregon Health & Science University. Dr. Buist obtained her medical degree from St Andrews University in Scotland, did her residency at the University of Colorado School of Medicine in Denver, and completed fellowships in pulmonary medicine and pulmonary physiology at the University of Oregon Medical School. Dr. Buist has been a member of numerous federal and international advisory groups. She is a past member of the New England Journal of Medicine Editorial Board and is a current member of the editorial board of Thorax and the Clinical Respiratory Journal. She has held numerous positions in the American Thoracic Society and was President in Dr. Buist's research interests are primarily in the areas of asthma and COPD, with particular emphasis on the epidemiology and management of these diseases. Dr. Buist, together with Dr. Jon Samet, started the ATS IRE Program in Since then, the program, now called the MECOR (Methods in Epidemiologic, Clinical & Operations Research) Program has been held annually in Latin America (Mexico, Chile, Brazil, Argentina, Peru, Uruguay and Ecuador). The MECOR Program began in Africa in 2007, in Turkey in 2008, and in India in 2009.

Stefano Guerra, MD, PhD Associate Professor, Medicine Dahlberg Chair, Pulmonary Medicine The University of Arizona 1501 N Campbell Ave Tucson, AZ 85724-5030 Phone: +1 520 626 7411 Dr Stefano Guerra

7 Stefano Guerra, MD, PhD Associate Professor, Medicine Dahlberg Chair, Pulmonary Medicine The University of Arizona 1501 N Campbell Ave Tucson, AZ Phone: Dr Stefano Guerra is an associate professor in Medicine and the Dahlberg Chair in Pulmonary Medicine at the University of Arizona in Tucson, AZ, and he also holds a joint appointment as associate professor at the CREAL Center in Barcelona, Spain. He received his MD from the University of Milan, Italy, and his Master in Public Health and PhD (Epidemiology / Genetics) from the University of Arizona, where he now teaches a graduate level course in genetic epidemiology. He is involved in several long-term cohort studies on respiratory diseases with a major focus on the genetic and molecular components of complex obstructive lung diseases, including asthma and COPD. Among these studies are the 40-year long adult cohort of the Tucson Epidemiological Study of Airway Obstructive Disease and the 32-year long Tucson Children's Respiratory Study, for both of which he acts as the principal investigator of biomarker-related projects. ÖZGE YILMAZ, MD Celal Bayar University Medical Faculty Department of Pediatric Allergy and Pulmonology Manisa, Turkey oyilmaz_76@hotmail.com Phone: Dr Özge Yılmaz is currently Associate professor of Pediatrics in Celal Bayar University Medical Faculty, Department of Pediatric Allergy and Pulmonology. She graduated from Hacettepe University Medical Faculty in 2001 and completed her Pediatric residency in 2007 in Celal Bayar University Medical Faculty, Manisa. She completed her fellowship in Pediatric Allergy at the same university in She was a student in the first three levels of MECOR courses between 2008 and 2011 in Turkey and she finished the Global MECOR course in She has worked as a teaching assistant in MECOR for two years and since last year she is working as a faculty. She is the secretary of Experimental Research Assembly of Turkish Thoracic Society and a member of School committee. She is currently a member of the Pediatrics Assembly planning committee and international relations committee of American Thoracic Society. Moreover, she is a member of European Respiratory Society and European Academy of Allergy and Clinical Immunology. Her work focuses on pathophysiological aspects of pediatric asthma and wheezing in children as well as the quality of life in pediatric allergic diseases. 4

Pinar Ay, MD, MPH Professor of Public Health Marmara University School of Medicine Department of Public Health Basibuyuk Mah. Maltepe Basıbuyuk Yolu Sok.

Ay graduated from Istanbul University School of Medicine in 1994. She got her MPH degree from Hadassah Braun School of Public Health and Community Medicine in 2000.

8 Pinar Ay, MD, MPH Professor of Public Health Marmara University School of Medicine Department of Public Health Basibuyuk Mah. Maltepe Basıbuyuk Yolu Sok. No:9/ Maltepe Istanbul - TURKEY npay@marmara.edu.tr Pinar Ay is a professor of Public Health at Marmara University, School of Medicine since Dr. Ay graduated from Istanbul University School of Medicine in She got her MPH degree from Hadassah Braun School of Public Health and Community Medicine in She completed her residency in Public Health at Istanbul University School of Medicine in Since then she has been working at Marmara University, School of Medicine Department of Public Health. Dr. Ay is the co-author of a book on Evidence- Based Medicine. Her research interests are epidemiology, biostatistics, evidence-based medicine, qualitative research methods, women s health, child health, health seeking behavior and community mental health. Canan Karaman, MD Pulmonary Disease Specialist Master Student at Basic Pulmonary Biology Programme Nizip Devlet Hastanesi, Nizip, Gaziantep Work: drcanankaraman@yahoo.com I'm a pulmonary diseases specialist. I had my medical school degree from Ege University School of Medicine in 2004 and I had a five year long education in Dokuz Eylul University School of Medicine, Department of Pulmonary Diseases. I worked on environmental and occupational medicine during my education in Dokuz Eylul University. I had studies on dental technicians pneumoconiosis, biomass exposure and spirometry standardization. I also made 3 studies on pulmonary arterial hypertension rat model. One of our studies had Pulmonary Circulation Award by Turkish Thoracic Society in I now live in Gaziantep and work in Nizip State Hospital. At the same time, I study on primary mesothelial cell cultures and cell lines in Gazinatep University School of Medicine Cell Culture Laboratory. I'm also a master student in Basic Respiratory Biology Programme. I had Level 3 in MECOR and as Sonia said: I'm a MECOR product :) 5

9 LEVEL 1 COMPETENCIES Overall Goals Level 1 is designed for academic physicians who will be involved in conducting medical research. Participants will learn the fundamentals of posing testable research questions, choosing among various study designs for generating and testing hypotheses, and develop basic bio-statistical skills. Participants will gain an understanding of statistics that will help them to collaborate effectively with statistical co-investigators. Epidemiology Descriptive Epidemiology Understand the basis of an epidemiologic approach to disease, e.g. populations, prevalence, incidence Research design Research Design Research Questions Become familiar with the major study types (cross-sectional, case-control, cohort, and clinical trial) and their respective measures of effect Be able to pose simple research questions and recognize the most appropriate study design for the question posed Research methods Sampling & Population Selection Sample Size & Power Questionnaires, Measures, & Measurement Procedures Quality Control Ethics & Informed Consent Study Proposal Stages Differentiate between populations and samples and understand how they may affect results Appreciate the importance of adequate power and the factors affecting power Comprehend valid and reliable measurements; sensitivity, specificity and predictive value Review techniques for maximizing data quality Value the Importance of ethical conduct of human research 1) One-sentence hypothesis 2) Two-page summary 3) Full proposal 4) Operations manual 6

10 Statistics LEVEL 1 COMPETENCIES Descriptive Statistics Measures of Association & Effect Sources of Error Univariate & Bivariate Analyses Summarize continuous and categorized data; understand and use measures of central tendency and measures of dispersion Understand prevalence, incidence, cumulative incidence, and their odds ratios Comprehend bias, confounding chance, Type I and Type 2 errors, standard error and confidence intervals Differentiate t-test and ANOVA; Wilcoxon and Kruskall-Wallis; chi-squared Multivariate Analyses Logistic Regression Understand the principles behind multiple linear regression Grasp the application of multiple logistic regression Reading & writing the presentation Reading a scientific paper Evidence-based medicine Writing a scientific paper Addressed in subsequent MECOR levels Addressed in subsequent MECOR levels Addressed in subsequent MECOR levels Presentation Protocol Present a research protocol developed during the course 7

11 PROTOCOL OUTLINE * 1. Title Clear and descriptive 2. Research Question One sentence concisely stating your question, answer by yes/no/number 3. Objective Overall purpose, primary and secondary objectives: statement 4. Hypothesis Anticipated results 5. Rationale/Background One to several paragraphs indicating why the question is important 6. Study Design Cross-sectional vs. case-control, vs. cohort, etc. (2x2 table) 7. Participants/Study Population Inclusion and exclusion criteria (location, age, sex etc.) Recruitment strategy/sampling Human subject informed consent and ethics review 8. Variables Outcome (dependent variable, response variable) Exposure (risk factor, independent variable, predictor, explanatory variable, treatment) Covariates and Confounders Data collection and quality control methods (questionnaire, medical record review, etc.) 9. Statistical Analysis Hypothesis Sample size and power Analytic Approach 10. Timeline Phases of research plan, recruitment, screening, data collection, follow up, data analysis, report preparation 11. Budget Personnel, Equipment, Travel, Materials, Publication Costs 12. Strengths and Weaknesses 13. Implications for Public Health * Adapted from Hulley et al.: Designing Clinical Research: An Epidemiologic Approach, Appendix 1.1, page 15 8

12 FINER CRITERIA FOR EVALUATING STUDY QUESTIONS Feasible Adequate number of subjects Adequate technical expertise Affordable in time and cost Manageable in scope Interesting To the investigator Novel Confirms or refutes previous findings Extends previous findings, such as to new geographic areas or populations Provides new findings Ethical Must pass institutional human subjects review board (IRB) Relevant To scientific knowledge To clinical and health policy (e.g., affects treatment or prevention) To future research (e.g., improves understanding of mechanism) What are the implications of finding out the answer to your question? Ibid, Table 2.1 9

13 2 X 2 TABLE FORMAT Outcome (dependent variable, response variable) (+) ( ) Exposure risk factor independent variable predictor explanatory variable treatment (+) ( ) 10

14 COURSE SCHEDULE MONDAY, 2 NOVEMBER TIME TOPIC FACULTY SLIDES 8:30 9:15 AM Welcome and Introduction to Course and Faculty: Plenary L1, 2, 3 Sonia 9:15 9:45AM 9:45 10:15 AM 10:15 10:30 AM Selecting a Research Question and FINER criteria: Plenary L1 and L2 10:30 11:00 AM Tea/Coffee Break Expectations, Student Introduction & Research Interest Study Design I: Overview and Cohort Studies and Incidence Sonia Trish Trish Group Assignments Slides: Research Question Slides: Introduction 11:00 12:00 PM Study Design I: (Continued) Trish Slides: Study Design I 12:00 1:00 PM 1:00 2:00 PM Lunch 2:00 3:00 PM 3:00 3:30 PM Small Groups: discussion on research question Literature search techniques & effective use of PubMed Plenary L1, 2, 3 Small Groups: discussion on research question (Continued) 3:30 4:00 PM Tea/Coffee Break 4:00 5:30 PM Homework Small Groups: Report back to full group with FINER criteria 1. Develop a draft of Research Question 2. Each student to select, read and review one journal article related to the research question. Dr. Sriganesh available for help. 3. Read Hulley Chapter 1,2, 7 4. Watch Video: Cohort studies, =PU3NGMKNj5o Pinar Due Tuesday AM 11

15 TUESDAY, 3 NOVEMBER TIME TOPIC FACULTY SLIDES 8:30 9:30 AM Population and Sample Selection Pinar 9:30 9:45 AM Quiz Ozge Slides: Sampling 9:45 10:45 AM 10:45 11:00 AM Tea/Coffee Break 11:00 12:00 PM Statistics I: Role of Statistics in Medical Research Study Design II: Cross Sectional Study Design/ Prevalence Trish Slides: Biostat 1 Sonia Slides: Study Design II 12:00 1:00 PM Study Design III: Case-Control Studies Ozge Slides: Study Design III 1:00 2:00 PM Lunch 2:00 3:00 PM Development of a Research Protocol Sonia 3:00 3:30 PM Small Groups: discussion on research question and study design (Continued) 3:30 4:00 PM Tea/Coffee Break 4:30 5:30 PM Homework Small Groups: Commence work on research protocol 1. Decision on Final Research Question 2. Decision on Study Design 2x2 Table 3. Write Protocol and PowerPoint: Title, Research Question, Significance, Design, Subjects (inclusion/exclusion) 4. Read Hulley Chapters 7, 8, Watch Video: Study Design Scenarios =SFKsNJOhbK8 6. Watch Video: Case/Control Studies =BQI2NjzPU68 Slides: Research Protocol Due Weds AM 12

16 WEDNESDAY, 4 NOVEMBER TIME TOPIC FACULTY SLIDES 8:30 9:30 AM Statistics 2: Confidence Intervals Stefano 9:30 9:45 AM Quiz Pinar Slides: Biostat 2 9:45 10:45 AM Questionnaires Ozge Slides: Questionnaires 10:45 11:00 AM Tea/Coffee Break 11:00 12:00 PM Measures of Association: RR and OR Ozge 12:00 1:00 PM Respiratory Disease Outcomes Sonia 1:00 2:00 PM Lunch Slides: Measures of Association Slides: Respiratory Outcomes 2:00 3:00 PM Statistics 3: Fundamentals of Testing Trish Slides: Biostat 3 3:00 3:30 PM Small Groups: Further work on protocols 3:30 4:00 PM Tea/Coffee Break 4:00 5:00 PM Small Groups: Further work on protocols 5:00-5:30 PM Progress report from small groups Homework 1. Write Protocol: subjects, recruitment, outcome, exposure, confounders, data collection, quality control 2. Prepare PowerPoint slides and written report 3. Read Hulley Chapter 3, 4, 9, 15 &17 4. Bias: =j8souco0yby Due Thurs AM 13

17 THURSDAY, 5 NOVEMBER TIME TOPIC FACULTY SLIDES 8:30 9:30 AM Research Ethics, Plenary L1, 2 and 3 Sonia 9:30 9:45 AM Quiz Stefano 9:45 10:45 AM Sources of Error: Bias, Confounding Canan Slides: Bias 10:45 11:15 AM Tea/Coffee Break 11:15 12:15 PM Sample Size and Power Calculations Stefano Slides: Sample Size 12:15 1:00 PM 1:00 2:00 PM Lunch Small Groups: Further work on protocol, Sample Size Calculations 2:00 3:00 PM Statistics 4: Which test to use? Stefano Biostats 4 3:00 3:30 PM Small Groups: Further work on protocol, Sample Size Calculations 3:30 4:00 PM Tea/Coffee Break 4:00 5:30 PM Homework Small Groups: Further work on protocol, Sample Size Calculations 1. Complete Protocol: statistical issues, hypothesis, sample size, power approach, budget 2. Prepare final PowerPoint slides 3. Complete draft of 2-page protocol 4. Hulley Chapter 5, 6, 10, 11, 14 Due Friday AM 14

18 FRIDAY, 6 NOVEMBER TIME TOPIC FACULTY SLIDES 8:30 9:30 AM Sonia s Presentation Skills & Secrets of Academic Success Sonia 9:30 9:45 AM Quiz Canan 9:45 10:45 AM Study Design IV: Clinical Trials Pinar Slides: Clinical Trials 10:45 11:15 AM Tea/Coffee Break 11:15 1:00 PM Small Groups: Finalize Protocols 1:00 2:00 PM Lunch and Complete Survey Monkey Trish 2:00 3:30 PM 3:30 4:00 PM 4:00 5:30 PM Small Groups: Finalize Presentation and Protocols, Allocate speaking roles to each member Tea/Coffee Break and Start Practice for each group with Sonia Small Groups: Practice Presentations to Faculty & each group with Sonia Due Friday PM Submit final 2-page protocol Homework Small Groups: Practice delivering presentation Sonia 15

19 SATURDAY, 7 NOVEMBER TIME TOPIC FACULTY READINGS* & SLIDES 8:30 10:30 AM Presentations 10:30 11:00 AM Tea/Coffee Break 11:00 1:00 PM Presentations 1:00 PM Graduation Lunch 16

Level 2 Course Syllabus

American Thoracic Society&Turkish Thoracic Society Methods in Epidemiologic, Clinical & Operations Research (MECOR) Level 2 Course Syllabus Çeşme, Turkey November 6, 2017 November 11, 2017 1 ACKNOWLEDGMENTS