1.     Racial & Sex Disparities in Lupus & Transplant Outcomes

Leads: Dr. Jorge Ortiz, Dr. Naoru Koizumi

Skills to be acquired: Basic Statistics, Survival Analysis by Sex and Ethnicity 

Background

Introduction to the problem (Approx. 10-min video introduction recorded by Dr. Ortiz will be played on July 22 covers below.)

1. Would you briefly explain Lupus or, more formally, Systemic Lupus Erythematosus (SLE), and how the disease could cause organ damage, particularly kidney failure?
2. Would you explain what we know about racial and sex disparities in Lupus?
3. Please explain what are unknowns about kidney transplant recipients whose kidneys failed as a result of Lupus, and also objective of the study?

Study objective

Lupus is often known as a disease for women with childbearing age. The progression of SLE, however, is reported to differ by sex and ethnicity, and a recent article states that minorities are more likely to progress to kidney and other organ failures as a result of SLE, thereby leading to a need for a transplant. The outcomes of transplants among these patients are unknown. We will see how the outcomes of kidney transplants differ by sex and ethicity in the transplant recipients with LSE diagnosis. Ref: https://onlinelibrary.wiley.com/doi/10.1002/acr.24892 (Lupus and Ethnicity)

Tasks

1. https://scholar.google.com/) and relevant keywords (e.g., kidney transplant, lupus) to select 5-10 most relevant articles (No need to be ambitious, select only those that are closely related to the study objective). Pick articles published only after 2010. Prepare half a page concise summary of what the team learned from the lit review. Send the team summary to Dr. Koizumi (nkoizumi@gmu.edu) by noon of July 29. (Week 1)
2. nkoizumi@gmu.edu) by noon of August 5.

2.     Optimal Immunosuppressive Regimen for Pediatric Liver Transplant Recipients

Leads: Dr. Geovanni Faddoul, Dr. Ali Andalibi, Dr. Naoru Koizumi

Skills to be acquired: Basic Statistics, Survival Analysis by immunosuppressive regimen 

Background

Introduction to the problem (Approx. 10-min introduction videos recorded by Dr. Faddoul and Dr. Andalibi will be played on July 22 covers below.)

Dr. Faddoul:

1. Would you briefly explain the basics of immunosuppression among transplant recipients? Why do they need it? Would you explain the basic mechanism of immunosuppression?
2. How do you immunosuppress patients, e.g., induction and maintenance phases?
3. Can you explain what kind of medications are currently used for the patients? Do they differ by transplant center? Can you explain key differences in induction medications used in transplantation: Antithymocyte globulin (Thymo), Alemtuzumab (Campath), Basiliximab, and Daclizumab?
4. Please explain objective of the study. What is the novelty of the study?

Dr. Andalibi:

1. Would you explain the basic mechanism of immunosuppression? In which treatment areas has immunosuppression been used?
2. Would you explain differences in immunological responses between adult and pediatric patients and why?
3. Could you explain pharmacokinetics of induction immunosuppressive drugs: Antithymocyte globulin (Thymo), Alemtuzumab (Campath), Basiliximab, and Daclizumab?

Study objective

Transplant recipients take a cocktail of immunosuppressive drugs rest of their lives (or until the organ fails) to reduce the risk of rejecting the organ transplanted. Managing immunosuppressive regimen (e.g., which medications to take and how much) is one of the big challenges that all transplant centers face as the optimal set and dose of drugs highly vary from patient to patient. There has been limited study on the best approach to manage immunosuppression in pediatric transplant recipients. We will investigate how transplant outcomes (graft failure and patient mortality) vary by induction drug (listed above) among pediatric liver transplant recipients. Ref. https://link.springer.com/chapter/10.1007/978-3-030-00132-2_4 (Download Chapter 4 from the bottom link “Download chapter PDF”)

Tasks

1. Perform a lit review on the effects of immunosuppression in pediatric (liver and other organ) transplant recipients. For the lit review, please use google scholar (https://scholar.google.com/) and relevant keywords (e.g., pediatric transplant, immunosuppression) to select 5-7 most relevant articles (No need to be ambitious, select only those that are strictly related to what we are doing). Use articles only after 2010 and those studies that report data analysis results (thus, no reviews or opinions). Prepare a 1/2 -page concise summary of what you learned.Send the team summary to Dr. Andalibi (aandalib@gmu.edu) by noon of July 29. (Week 1)
2. The team will be analyzing data to see whether transplant outcomes (graft failure and patient mortality) differ by the induction medication used, after controlling for other key factors (age, ethnicity etc.). We will examine this by performing a survival (Kaplan Meier or KM) analysis. (Week 2 – Task A). We will also compare patient characteristics (age, sex, ethnicity, induction and maintenance medications used, etc.) between the transplant recipients who have experienced graft failure and those who have not. For this, we will prepare a descriptive table using t- and chi-sq. tests. Dr. Nayebpour will provide the data and the R codes to perform these on July 29.  Send the team results to Dr. Koizumi (nkoizumi@gmu.edu) by noon of August 5.
3. The team will interpret the results and prepare a summary of findings and presentation slides (Week 3). Dr. Koizumi will lecture basic statistics to help interpret your results and statistical theories behind the analyses on Aug. 5. Bring the draft team slides to the Zoom class on August 12.

3.     Advance Care Planning

Leads: Dr. Megumi Inoue, Dr. Meng-Hao Li, Mr. Zifu Wang 

Skills to be acquired: Basic Statistics, Mapping 

Background

Introduction to the problem (10-min interview video will be played on July 22 covering below.)

1. Would you briefly explain what Advance Care Planning (ACP) means? What is it? What kind of people use it? And how it is implemented?
2. Would you explain what kind of research has been done on the topic of ACP?
3. Please explain objective of the study, and what kind of knowledge gap the study is filling.

Study objective

Advance Care Planning is the process of planning for future medical care in the event that a person becomes unable to make decisions or speak for oneself. We will examine how advanced care planning registration rate differs by counties across US to derive policy implications. Ref: https://www.cms.gov/outreach-and-education/medicare-learning-network-mln/mlnproducts/downloads/advancecareplanning.pdf

Tasks

1. Conduct a literature review and summarize the current knowledge on engagement in advance directives (Ads) in relation to geographical differences (e.g., rural vs. urban, different states), as well as individuals’ family structure (e.g., marital status, kinless, childless). To conduct the literature review, please use google scholar (https://scholar.google.com/) and relevant keywords (e.g., advance directives, living will, durable power of attorney for health care). Select 5-7 most relevant articles for each (geographical differences and family structure). You need not to be overly ambitious; choose articles that are strictly related to our research questions. Focus on articles published after 2010 that provide data analysis results. Prepare a 1/2 -page concise summary of what you learned.Send the team summary to Dr. Inoue (minoue2@gmu.edu) by noon of July 29. (Week 1)
2. We would like to investigate if individuals’’ geographical locations and family structure along with other characteristics are correlated with the likelihood of engagement in ADs using the data from the Health and Retirement Study. We will examine this using descriptive statistics involving t- and chi-sq. tests (Week 2). Mr. Baxter and Mr. Wang will provide data and tutorial to create tables and maps on July 29.  Send the team results to Dr. Inoue (minoue2@gmu.edu) AND Dr. Li (mli11@gmu.edu) by noon of August 5.
3. The team will interpret the results and prepare a summary of findings and presentation slides (Week 3). Dr. Koizumi will lecture basic statistics to help interpret your results and statistical theories behind the analyses on Aug. 5. Bring the draft team slides to the Zoom class on August 12.

4.    Gut Microbiome and Kidney Transplant

Leads: Dr. Mehdi Nayebpour, Dr. Meng-Hao Li

Skills to be acquired: Basic Statistics, Network Visualization

Background

Introduction in person on July 22 (Will be videotaped and distributed later)

Study objective

Gut microbiome composition and its impact on human health vary depending on the host’s characteristics (sex, ethnicity, and socio-economic backgrounds of the hosts). We will be examining how the composition of gut microbiome community differs by socio-economic background of transplant recipients and if it has an impact on kidney transplant outcomes. We will suggest policies to mitigate such health disparities among different socio-economic groups. Using the real data, we will perform a network analysis to cluster microbiome genera that tend to move together and find meaningful patterns.

Tasks

1. Read the papers given to you to become familiar with a. the gut microbiome and its role in humane health (Ref.1), b. the role of gut microbiome in kidney disease (Ref.2), c. ways to mitigate and repair the gut microbiome and its limitations (Ref.3). Review the questions and send your answers to Dr. Nayebpour (m.nayebpour@gmail.com) by noon of July 29. (Week 1)
2. Read the given paper about microbiome networks then familiarize yourself using an example in R. https://pubmed.ncbi.nlm.nih.gov/26576770/ (Microbiome networks). Now we deal with real data collected from real kidney transplant recipients. First divide the patients by their socio-economic status using insurance type (private vs. non-private). Use a t-test to compare the gut microbiome diversity after and before the transplant surgery for each insurance group. Then use the network analysis technique you learned in R and examine whether or not clusters of bacterial genera tend to increase/decrease together after a kidney transplant surgery. Dr. Li will provide the data and the R codes to perform these on July 29. Send the team results to Dr. Li (mli11@gmu.edu) by noon of August 5. (Week 2)
3. If a significant cluster of bacterial genera is detected in your analysis above, search the web and see if such bacterial genera possess a critical role in kidney health Furthermore, search the web to find techniques to remedy and repair gut microbiome deficiencies. Finally, add your own thoughts and suggest policies on how we can increase gut microbiome health for lower socio-economic groups. The team will prepare a summary of findings and presentation slides (Week 3). Dr. Koizumi will lecture basic statistics to help interpret your results and statistical theories behind the analyses on Aug. 5. Bring the draft team slides to the Zoom class on August 12.

5.    Harmful Algal Bloom Trends

Leads: Dr. Jim Olds, Dr. Nadine Kabbani, Mr. Patrick Baxter

Skills to be acquired: Data processing, Mapping

Background

Introduction in person on July 22 (videotaped and distributed later)

Study objective

Cyanotoxins are produced by Harmful Algal Blooms (HABS). HABS occur in fresh and salt water bodies of significance such as Lake Eire and the Chesapeake Bay and adversely affect the public health and our local economies.  The team will examine how US HAB outbreaks vary by season, year, and region (census division) using the USEPA dataset (https://catalog.data.gov/dataset/cyanobacteria-state-reported-events-and-recreation-advisories). Ref. https://www.cdc.gov/habs/pdf/habsphysician_card.pdf (for cyanobacteria basics) and https://health.wyo.gov/wp-content/uploads/2022/05/cyanobacterial-blooms-and-associated-illnesses-presentation.pdf (for cyanobacteria related illnesses)

Tasks

1. Do a lit review on cyanobacteria illnesses and epidemiological studies of the illnesses. For the lit review, please use google scholar (https://scholar.google.com/) and relevant keywords (e.g., cyanobacteria, prevalence, epidemiology, hospitalization etc.) to select 5-7 most relevant articles (No need to be ambitious, select only those that are strictly related to what we are doing). If possible, find US-based studies. Prepare a 1/2 -page concise summary of what you learned.Send the team summary to Dr. Olds (jolds@gmu.edu) AND Dr. Kabbani (nkabbani@gmu.edu) by noon of July 29. (Week 1)
2. We will investigate the seasonal and geographical trends of different algal blooms and cyanobacteria/cyanotoxins outbreaks. Generate graphs and maps showing seasonal and spatial trends of differing algae bloom by year (Week 2 – Task A). We would also like to see how these blooms vary by season and region. For this, prepare a descriptive table and test the regional differences using ANOVA (Week 2 – Task B). Mr. Baxter and Mr. Wang will provide data and tutorial to create tables and maps on July 29. Send the team results to Dr. Olds (jolds@gmu.edu), Mr. Baxter (pbaxter2@gmu.edu), AND Mr. Wang (zwang31@gmu.edu) by noon of August 5. (Week 2)
3. The team will interpret the results and prepare a summary of findings and presentation slides (Week 3). Bring the draft team slides to the Zoom class on August 12.

6.    Transplant Tourism: Country Network Analysis

Leads: Dr. Naoru Koizumi, Mr. Raj Kulkarni

Skills to be acquired: Data collection and processing, Network Visualization

Background

Introduction to the problem (the 10-min interview video played on July 22 covers below.)

1. Would you briefly explain what kidney trade or kidney trafficking means? What is it? Why is it a problem?
2. Would you explain what kind of research has been done on the topic?
3. Please explain objective of the study, and what kind of knowledge gap the study is filling.

Study objective

Kidney sales is illegal in most countries. Illegal kidney sales as well as transplant tourism have been on the rise, however, being facilitated by transnational crime organizations, poverty and wars, and chronic shortage of kidney donors. We will generate longitudinal networks of seller, buyer, broker, and surgery counties using unique data collected through webscraping of news articles between 2000 and 2021. Ref: https://gh.bmj.com/content/7/9/e009803.abstract (Global kidney trade networks)

Tasks

1. Perform a google or other search to find out country-level policies on kidney sales. Currently, Iran is the only country in the world that allows kidney sales. Other countries, such as China and the Philippines, allowed kidney sales in the past. Please fill the table in the excel file as much as you can. Afghanistan row is filled for your reference. If no information can be found, please leave the cells empty. Send the team summary to Dr. Koizumi (nkoizumi@gmu.edu) by noon of July 29. (Week 1)
2. We have created the dataset recording kidney sellers’ and buyers’ nationalities as well as where the surgeries took place.  Create country networks showing the connections between: a) buyer and seller countries; b) seller and surgery countries; and c) buyer and surgery countries by 5-year period (2000-2004; 2005-2009; 2010-2014; >2014) using Gephi. Mr. Kulkarni will provide the Gephi tutorial on July 29. Send the team results to Dr. Koizumi (nkoizumi@gmu.edu) AND Mr. Kulkarni (rkulkarn@gmu.edu) by noon of August 5. (Week 2)
3. The team will interpret the results and prepare a summary of findings and presentation slides. Please provide your insights about the characteristics of the countries providing sellers, buyers and surgeries respectively. What kind of countries are more likely to provide sellers, buyers or perform surgeries (Week 3). Bring the draft team slides to the Zoom class on August 12.

7.    Viruses and Host Membranes

Leads Dr. Nadine Kabbani, Dr. Jim Olds

Skills to be acquired: Data collection, Bibliometrics.

Background

Introduction in person on July 22 (videotaped and distributed later)

Study objective

Viral particles need to first gain a foothold for attachment on the surface of the host cell to gain molecular entry during infection. The distinction between the processes that drive entry from those that mediate attachment for various animal infecting viruses remains obscure in the scientific literature. Important questions exist: which specific molecules (proteins, lipid, or sugars) are involved in attachment or entry? How do these interactions differ by virus type?

In this project, we will explore emerging discoveries on the nature of viral attachment and entry within the scientific literature focusing on the zoonotic and highly infective rabies virus. The objective is to develop a comprehensive understanding of mechanisms for infectivity (attachment and entry) by defining the landscape of rabies virus research through bibliometric analysis. Building on published work we will examine scientific evidence that supports the concept of an evolutionarily conserved host cell targeting mechanism responsible for rabies infection and disease in humans as well as other species:

Tasks

1. Conduct a comprehensive literature review using google scholar (https://scholar.google.com/) and PubMed. Identify all relevant keywords (e.g., rabies virus, neuromuscular synapse) and create an annotated bibliography. Prepare a 1/2 -page concise summary of what you learned.Send the team summary to Dr. Berg (lberg4@gmu.edu), Dr. Olds (jolds@gmu.edu) AND Dr. Kabbani (nkabbani@gmu.edu) by noon of July 29. (Week 1)
2. Using the annotated bibliography examine the following using descriptive statistics involving t- and chi-sq. tests (Week 2) andR codes to perform these on July 29. 
   • Topic trends in rabies virus research (e.g., behavior, species (dogs, foxes, humans))
   • Scientists and Networks involved in rabies virus research (e.g., zoology, neuroscience, etc.)
   • Overlap, segregation, and interactions between knowledge domains in rabies virus research (e.g., nicotinic receptor pathways of addiction in brain and rabies virus signaling at neuromuscular junction)
   • Send the team results to Dr. Berg (lberg4@gmu.edu), Dr. Dr. Olds (jolds@gmu.edu) AND Dr. Kabbani (nkabbani@gmu.edu) by noon of August 5.
3. Collectively (with others in the Group) graph and interpret the results and prepare a summary of findings and presentation slides (Week 3). Bring the draft team slides to the Zoom class on August 12.