Andrew Craver
Project Personnel, University of Chicago
16 active projects
Duplicate of Neglected Infections of Poverty - Up on EHS
Scientific Questions Being Studied
In this project, NIEHS R25 Up on EHS undergraduate trainees and UChicago IPPH staff members will define, describe, and map the neglected infections of poverty in the USA. The neglected infections of poverty are understudied, poorly-understood, and yet can be highly detrimental to human health and productive capacity. We hope to build some awareness of these infections while teaching students how to use the Workbench and its associated data management and analysis tools and techniques.
Project Purpose(s)
- Educational
Scientific Approaches
We will use demographic, zip/socioeconomic, condition, and lab/measurement data to explore and characterize these infections. We may also look for additional comorbidities. We will map the data to US census shapefiles at the 3-digit zip code prefix level using R mapping packages and Geopandas. We will use descriptive and inferential statistics in Python and R.
Anticipated Findings
We anticipate that we will find small to medium-sized Ns of the neglected infections of poverty, and we wonder if their geographic distributions will reveal clear patterns. Our descriptive stats will contribute to science by providing an overview of the number of cases and demographic/socioeconomic characteristics of participants who have had these infections. The literature on these infections is limited, and so we hope that our exploration will yield some value and contribute to this underdeveloped body of work.
Demographic Categories of Interest
- Race / Ethnicity
- Geography
- Access to Care
- Education Level
- Income Level
Data Set Used
Controlled Tier
Neglected Infections of Poverty - Up on EHS
Scientific Questions Being Studied
In this project, NIEHS R25 Up on EHS undergraduate trainees and UChicago IPPH staff members will define, describe, and map the neglected infections of poverty in the USA. The neglected infections of poverty are understudied, poorly-understood, and yet can be highly detrimental to human health and productive capacity. We hope to build some awareness of these infections while teaching students how to use the Workbench and its associated data management and analysis tools and techniques.
Project Purpose(s)
- Educational
Scientific Approaches
We will use demographic, zip/socioeconomic, condition, and lab/measurement data to explore and characterize these infections. We may also look for additional comorbidities. We will map the data to US census shapefiles at the 3-digit zip code prefix level using R mapping packages and Geopandas. We will use descriptive and inferential statistics in Python and R.
Anticipated Findings
We anticipate that we will find small to medium-sized Ns of the neglected infections of poverty, and we wonder if their geographic distributions will reveal clear patterns. Our descriptive stats will contribute to science by providing an overview of the number of cases and demographic/socioeconomic characteristics of participants who have had these infections. The literature on these infections is limited, and so we hope that our exploration will yield some value and contribute to this underdeveloped body of work.
Demographic Categories of Interest
- Race / Ethnicity
- Geography
- Access to Care
- Education Level
- Income Level
Data Set Used
Controlled TierResearch Team
Owner:
- Temitope Creppy - Undergraduate Student, University of Chicago
- Olga Lesnik - Project Personnel, University of Chicago
- Lara Kowalcyk - Undergraduate Student, University of Chicago
- Hannah Li - Undergraduate Student, University of Chicago
- Katherine Goscilo - Early Career Tenure-track Researcher, University of Chicago
- Arielle Fishman - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Asthma Paper
Scientific Questions Being Studied
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Project Purpose(s)
- Disease Focused Research (hypertension)
- Population Health
Scientific Approaches
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Anticipated Findings
We anticipate an association between air pollution concentrations and the incidence of hypertension. We anticipate that the strength of this association will vary by race and other demographic factors, as well as by smoking status and other behavioral health factors.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierCardio Paper Working Version
Scientific Questions Being Studied
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Project Purpose(s)
- Disease Focused Research (hypertension)
- Population Health
Scientific Approaches
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Anticipated Findings
We anticipate an association between air pollution concentrations and the incidence of hypertension. We anticipate that the strength of this association will vary by race and other demographic factors, as well as by smoking status and other behavioral health factors.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Maia Griffith - Project Personnel, University of Chicago
- Jiajun Luo - Research Fellow, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Temi Project - Up on EHS
Scientific Questions Being Studied
This workspace will be shared with students (all are registered Workbench users with their own accounts) as they work through their quarter-long Equity in Precision Health research project at the University of Chicago. These students are investigating a variety of associations between conditions, treatments, and demographics in order to learn how to use the Workbench while exploring health equity. I will give them a head start by unpacking some of the data for them and showing them how to clean and analyze data.
Project Purpose(s)
- Educational
Scientific Approaches
This workspace will be shared with students (all are registered Workbench users with their own accounts) as they work through their quarter-long Equity in Precision Health research project at the University of Chicago. These students are investigating a variety of associations between conditions, treatments, and demographics in order to learn how to use the Workbench while exploring health equity. I will give them a head start by unpacking some of the data for them and showing them how to clean and analyze data.
Anticipated Findings
We hope that students will develop an understanding of the Workbench, its methods, the available data, and the process of undertaking a Workbench project from start to finish.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Temitope Creppy - Undergraduate Student, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Practice Cohort view
Scientific Questions Being Studied
This workspace will be for educational purpose of working with All of Us Data for a student.
Project Purpose(s)
- Social / Behavioral
- Educational
Scientific Approaches
This workspace will be for educational purpose of working with All of Us Data for a student.
Anticipated Findings
This workspace will be for educational purpose of working with All of Us Data for a student.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Olga Lesnik - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Cancer and the Environment Revision
Scientific Questions Being Studied
The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of the relationship between PM2.5 and cardiometabolic outcomes in the AoU dataset, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project.
Project Purpose(s)
- Other Purpose (The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of PM2.5 and cardiometabolic outcomes, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project. )
Scientific Approaches
Regression analysis and other methods to be determined by the data.
The purpose of this workspace is to have a look at any environmental health variables included at the Controlled Tier. Our group hopes to be able to conduct an analysis of the relationship between PM2.5 and cardiometabolic outcomes in the AoU dataset, and we will create a new workspace with our research plan once we have a better idea of whether the dataset has the necessary variables to support this project.
Anticipated Findings
We hope to gain a better understanding of any associations between environmental PM 2.5 and cardiometabolic outcomes among the All of Us cohort. Such an analysis with a sample of this size would be a novel addition to the environmental health literature.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Maia Griffith - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
William Project - Andy Version
Scientific Questions Being Studied
I am creating a workspace as part as of the Equity and Precision health Spring 2023 Quarter course at the University of Chicago. I am a masters student in the Precision health program. I am learning to use the workbench. I plan to update this description as I frame my research question.
Project Purpose(s)
- Educational
Scientific Approaches
I am going to explore a question of equity in precision health using all available data in the workbench. I will refine my data and analytical requirements as I frame my research question.
Anticipated Findings
I am unclear what to anticipate. This is mainly a class exercise to understand how to use the workbench.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- William Olaprath - Graduate Trainee, University of Chicago
- Maia Griffith - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Olga Summer Project
Scientific Questions Being Studied
This project is for educational purposes - an Up on EHS student at the University of Chicago is learning how to use the workbench by investigating sinusitis cases
Project Purpose(s)
- Educational
Scientific Approaches
This project is for educational purposes - an Up on EHS student at the University of Chicago is learning how to use the workbench by investigating sinusitis cases
Anticipated Findings
This project is for educational purposes - an Up on EHS student at the University of Chicago is learning how to use the workbench by investigating sinusitis cases
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Olga Lesnik - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
William O - Equity in Precision Health
Scientific Questions Being Studied
I am creating a workspace as part as of the Equity and Precision health Spring 2023 Quarter course at the University of Chicago. I am a masters student in the Precision health program. I am learning to use the workbench. I plan to update this description as I frame my research question.
Project Purpose(s)
- Educational
Scientific Approaches
I am going to explore a question of equity in precision health using all available data in the workbench. I will refine my data and analytical requirements as I frame my research question.
Anticipated Findings
I am unclear what to anticipate. This is mainly a class exercise to understand how to use the workbench.
Demographic Categories of Interest
- Geography
- Access to Care
- Education Level
- Income Level
Data Set Used
Controlled TierResearch Team
Owner:
- William Olaprath - Graduate Trainee, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Cardio Paper
Scientific Questions Being Studied
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Project Purpose(s)
- Disease Focused Research (hypertension)
- Population Health
Scientific Approaches
This study seeks to understand the relationship between ambient air pollution concentrations (PM2.5 and NO2) and the incidence of hypertension in the All of Us cohort. To explore this association we will match modelled air quality data for the continental USA to participant zip code prefix. Analysis will consist of multivariate logistic regression and generalized additive models.
Anticipated Findings
We anticipate an association between air pollution concentrations and the incidence of hypertension. We anticipate that the strength of this association will vary by race and other demographic factors, as well as by smoking status and other behavioral health factors.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Maia Griffith - Project Personnel, University of Chicago
- Jiajun Luo - Research Fellow, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Long COVID
Scientific Questions Being Studied
We will see if we can identify a cohort of AoU participants who meet the case definition of Long COVID as defined by Thaweethai et al, JAMA 2023. Long COVID is a currently public health concern and may continue to be significant in the future. Identifying those who may have Long COVID in the AoU dataset will be an important first step toward follow up on their long-term health outcomes.
Project Purpose(s)
- Disease Focused Research (Long COVID)
Scientific Approaches
Our work will be mainly descriptive. We will create a case definition using standard data builder queries to understand the N of those who may have long COVID, their comorbidities, and their sociodemographic characteristics.
Anticipated Findings
We anticipate that we will not be able to find the exact criteria outlined in Thaweethai et al, but that we will find significant overlap. We anticipate that using an amended case definition, we will be able to to find a cohort of participants with possible Long COVID.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierPrior_William O - Equity in Precision Health
Scientific Questions Being Studied
I am creating a workspace as part as of the Equity and Precision health Spring 2023 Quarter course at the University of Chicago. I am a masters student in the Precision health program. I am learning to use the workbench. I plan to update this description as I frame my research question.
Project Purpose(s)
- Educational
Scientific Approaches
I am going to explore a question of equity in precision health using all available data in the workbench. I will refine my data and analytical requirements as I frame my research question.
Anticipated Findings
I am unclear what to anticipate. This is mainly a class exercise to understand how to use the workbench.
Demographic Categories of Interest
- Geography
- Access to Care
- Education Level
- Income Level
Data Set Used
Controlled TierResearch Team
Owner:
- William Olaprath - Graduate Trainee, University of Chicago
- Maia Griffith - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Shana Summer Work
Scientific Questions Being Studied
IPPH Summer Intern Shana Littleton will use this workspace to learn how to use the All of Us Researcher Workbench. The purpose of this workspace is probably purely educational.
Project Purpose(s)
- Educational
Scientific Approaches
IPPH Summer Intern Shana Littleton will use this workspace to learn how to use the All of Us Researcher Workbench. The purpose of this workspace is probably purely educational.
Anticipated Findings
IPPH Summer Intern Shana Littleton will use this workspace to learn how to use the All of Us Researcher Workbench. The purpose of this workspace is probably purely educational. There are no anticipated findings.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierResearch Team
Owner:
- Shana Littleton - Graduate Trainee, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
Duplicate of How to Work with All of Us Genomic Data (Hail - Plink)(v7)
Scientific Questions Being Studied
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Project Purpose(s)
- Other Purpose (Demonstrate to the All of Us Researcher Workbench users how to get started with the All of Us genomic data and tools. It includes an overview of all the All of Us genomic data and shows some simple examples on how to use these data.)
Scientific Approaches
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Anticipated Findings
Not applicable - these notebooks demonstrate example analysis how to use Hail and PLINK to perform genome-wide association studies using the All of Us genomic data and phenotypic data.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Controlled TierSocial Determinants - Chicago
Scientific Questions Being Studied
We intend to provide descriptive data on the All of Us research cohort from the Chicagoland area, focusing specifically on social determinants of health.
Project Purpose(s)
- Educational
Scientific Approaches
Participants will be filtered to those that live in the Chicago area, and Jupyter notebook will be used to provide descriptive statistics using Python.
Anticipated Findings
Findings from this study will help to inform recruitment strategies for the area.
Demographic Categories of Interest
- Race / Ethnicity
- Access to Care
- Income Level
Data Set Used
Controlled TierResearch Team
Owner:
- Maia Griffith - Project Personnel, University of Chicago
- Andrew Craver - Project Personnel, University of Chicago
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