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Summer Research Program Home

Kaja Abbas, PhD

 

Kaja Abbas, PhD 

 

Assistant Professor of Infectious Diseases in Public Health
Department of Population Health Sciences
Virginia-Maryland Regional College of Veterinary Medicine
Virginia Tech

Project Title: "Systems Modeling of Latent Tuberculosis Treatment for South Africa"

 

 


 

Philana LinPhilana Lin, MD, MSC 

 

University of Pittsburgh Physicians Faculty
Department of Pediatrics and Research
Pediatric Infectious Disease

 

Seven researchers were awarded MIDAS Pilot Grants in 2011. Five faculty members were awarded "Developmental Awards," which carry a maximum award of $20,000 annually and provide researchers the opportunity to develop techniques or novel approaches to compuational modeling and simluation. Developmental grants may be awarded to investigators from various backgrounds and training who may be new to the field of infectious disease modeling. Two post-doctoral fellows were granted "Seed Awards," which provides them with up to $5,000 annually to conduct research on computational modeling and simulation of infectious diseases. Seed awardees must specify a senior investigator from the University of Pittsburgh's MIDAS National Center of Excellence, who serves as a mentor and co-investigator on the project.

Please read below to learn more about the awardees and their projects. 

Developmental Awards 


Hasan Guclu, PhD guclu

Department of Biostatistics
University of Pittsburgh

Project Title: "A Unified Framework for Modeling Infectious Diseases in Aging Populations with Decaying Immunity"

Abstract: This project aims to provide a convenient and effective modeling framework for risk analysis and policy making for long-term control of infectious diseases such as influenza, measles, and dengue fever. This framework combines the longitudinal demographic data such as the rate of births and deaths and aging in the population, and the social changes such as relocation and migration with the lack or decay of immunity in individuals. This project will fill a gap between these different modeling efforts and serve as a practical tool to test the effectiveness of various countermeasures. The specific tasks of the project will rely on accurate demographic data, theoretical foundations for the immunity modeling, high-performance agent-based simulations and social network analysis.


Louis Luangkesorn, PhD 

louis

Department of Industrial Engineering
University of Pittsburgh

Project Title: "Development of Statistical Methods to More Effectively Inform Policy Analysis Using Agent-Based Simulation Models of Infectious Diseases"

Abstract: Compared to other modeling methods, agent based simulation is able to model a system in greater detail including relationships between individual agents who are able to gather information about their environment and make independent decisions. However, this makes agent based models computationally intensive, making modelers slower to be able to respond to policy maker queries. Other modeling communities have employed methods based on statistical design of experiments to efficiently reach conclusions on the efficacy of interventions into the system. Currently, these questions are addressed in the practice of agent based models through the application of sensitivity analysis techniques. This project proposes to identify and implement design of experiment/optimization via simulation methods to MIDAS infectious disease models for use in policy analysis and evaluation. This identification will be made based on characteristics of the model/system under study as well as the question that the model is intended to address. Specifically, this project will be in conjunction with ongoing work within MIDAS by the PHICOR group on inter-hospital spread of MRSA. Successful completion of the pilot project will improve the support MIDAS provides to public health policy makers improving the ability of MIDAS modelers to respond to policy maker queries and requests.


Eunha Shim, PhD e_shim

Department of Epidemiology
University of Pittsburgh

Project Title: "Influence of Risk Perception on Vaccine Behavior: Rotavirus Vaccination as an Example" 

Abstract: Coming Soon.


 

 


Aarti Singh, PhDAartiSingh

Department of Machine Learning
Carnegie Mellon University 

Project Title: "Using Non-Local Connectivity Information to Identify Nascent Disease Outbreaks"

Abstract: This proposal seeks to develop computationally and statistically efficient procedures for detecting epidemics, such as influenza and MRSA (methicillin-resistant Staphylococcus aureus), in their nascent stages by leveraging non-local connectivity between geographically disparate locations. Recent studies suggest that disease spreading pathways are highly non-local in today's globalized world, e.g. due to ever-increasing volume of air traffic, patient transfers across different hospitals, etc. Most state-of-the-art disease outbreak detection methods use the gravity model to fuse data from local nearby regions. Such methods are plagued with high false alarm rates and poor detection capabilities, particularly when trying to identify an outbreak in its formative stages from crude and unreliable indicators that may not be statistically significant in any spatial region. The proposed research aims to achieve the following two goals: 1) Identify the occurrence of an influenza or MRSA outbreak in its nascent stages by projecting data onto an appropriate basis that is adapted to the structure of the non-local connectivity graph between geographically disparate regions/hospitals. 2) Learn the non-local connectivity graph which influences spread of the influenza virus or MRSA between different locations.

Larry Wasserman, PhD larry

Department of Statistics
Carnegie Mellon University 

Project Title: "Solving the NowCasting Problem" 

Abstract: In many epidemiological settings, knowing the true daily incidence of an infectious disease can be tremendously useful in predicting its future course and in optimizing public health intervention. It is especially helpful to be able to estimate daily incidence in real time. This has been dubbed the "NowCasting" problem. While direct measurement of disease incidence is practically impossible, we do have access to many data streams that are correlated with Influenza incidence. These data streams differ in their time granularity (from daily to weekly), their geographic granularity (from zipcode-level to U.S. Regional) and in their sampling procedure and completeness. However, they all contain some information about daily Influenza incidence. We propose to develop a principled solution to the Influenza NowCasting problem, based on a combination of statistical methodology and machine learning techniques. We seek a solution that can combine available data streams of any time and geographic granularity in a unified modeling framework.


Seed Awards

Supriya Kumar, PhDSupriya

Department of Epidemiology
University of Pittsburgh

Project Title: " Explaining the Mechanism Behind Persistent Racial Disparities in Influenza Vaccine Uptake." 

Abstract: From 2000 to 2010, consistently fewer Blacks over the age of 65 years got the seasonal influenza vaccine compared to Whites aged greater than 65 years in the US. Economic, geographic, and attitudinal barriers to vaccines among minorities have been proposed as reasons for disparities, but the mechanisms by which these factors could lead to the rates of uptake by race seen in the population have not been elucidated. Because surveys are rarely able to simultaneously capture the impacts of individual, geographic, and social network factors, and unable to capture feedbacks from multiple levels on individual vaccination behavior over time, we propose to build an agent-based model of Allegheny County in which individual agents make vaccine uptake decisions based on inputs from multiple sources. Agents with individual-level attributes, including demographic factors, employment status, and health insurance will update their attitude toward the vaccine daily as a function of feedbacks from pharmaceutical advertisements of vaccine and the attitudes of others in their social network. The resulting rates of vaccine uptake by race will be compared to rates seen in the Allegheny County Behavioral Risk Factor Surveillance System; such a model will allow us to not only elucidate a plausible mechanism that could cause the observed disparities, but also lead to future studies on the structure of influential social networks in such decision-making and reciprocal determinism between population-level vaccine uptake and the location of pharmacies in neighborhoods.


Olabisi Ojo, PhDbisi

Department of Microbiology and Molecular Genetics
University of Pittsburgh

Project Title: Agent Based Modeling of Tuberculosis Transmission in Allegheny County: a Pilot Evaluation" 

Abstract: Tuberculosis (TB) is an infectious disease found in humans and animals. It is mainly aerogenically transmitted between individuals as they intermingle in different communities. It has more recently become a worldwide research priority due to re-emergence in the developed world and co-infection with Human Immunodeficiency Virus-Acquired Immune Deficiency Syndrome especially in TB endemic countries. Modeling of infectious agents incorporates computational simulation of infectious diseases events to decipher different aspects of disease dynamics. The aims of this proposal are to carry out primary exploration of literature, data and tools learning for modeling TB transmission via the agency of the aerosol droplet by constructing an Agent Based Model (ABM), in the Allegheny County, Pennsylvania. Current data will be collected from health units from Allegheny County, to drive the proposed model. Each computer agent will represent a virtual person, discrete entities, with a potential for TB infection status, capable of moving among the general community for each of the simulated features. The ABM will be parameterized with probabilities of features of an artificial population. The ABM will be implemented in NetLogo® and the modeling proprietary software developed by the University of Pittsburgh Supercomputing core. It is expected that the model will be calibrated and the impact of this could therefore be evaluated by the introduction of preventive strategies, results of which could be potentially utilized in public health decision making. It is expected that the primary data generated from this project would be developed into a future grant application.

 

Check back for future announcements.

The University of Pittsburgh MIDAS National Center of Excellence is pleased to announce a Pilot Research Grant Program designed to facilitate collaborative research in computational modeling and simulation of infectious diseases. Investigators within the various schools, departments, and centers at the University of Pittsburgh, University of Pittsburgh Medical Center (UPMC), the RAND-University of Pittsburgh Health Institute (RUPHI), affiliated Institutions associated with the University of Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network are eligible to participate.

 

Download a printable copy of the RFA by clicking here.

Purpose 

Types of Proposals 

1. Seed Grants

Information

Eligibility

Budget

2. Development Grants

Information

Eligibility

Budget

Application Process

Resources

Review Considerations

Submission, Review and Award

Obligations of Awardees

Questions Regarding the Program

 

Purpose:

The Pilot Research Grant Program is designed to provide financial support for pilot research projects that will foster innovative research and attract new investigators to the field of infectious disease modeling and simulation. Preference will be given to projects that bring novel approaches and/or expertise to complex problems within the field of infectious disease modeling and simulation including, but not limited to, environmental influences, social networks, human behavioral change, policy, and economics, among other fields.

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Types of proposals

Two types of proposals will be accepted: Seed Grants and Development Grants.

MIDAS Seed Grants

Seed Grant Information  

  1. Seed Grants are intended to engage postdoctoral fellows as new investigators in computational modeling and simulation of infectious diseases.
  2. Maximum award of $5,000 (direct costs) annually with the possibility of renewal.
  3. Eligibility is restricted to postdoctoral fellows with an active interest in computational modeling and simulation of infectious disease research.
  4. An established investigator affiliated with the Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network must serve as a co-investigator.
  5. A letter of support from the postdoctoral applicant’s current research faculty mentor is required.

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Eligibility

  1. The Principal Investigator is required to be a full-time postdoctoral trainee/fellow from any school, department, or center at the University of Pittsburgh, UPMC, RUPHI, affiliated Institution associated with the University of Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network.
  2. One of the goals of the pilot research program is to assist postdoctoral fellows who are new to the field in obtaining experience in computational modeling and simulation of infectious diseases; therefore, one of the investigators must be established in a field of research that is relevant to the proposed work. That is, one investigator who is affiliated with the University of Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network must be able to mentor the more junior investigator, as appropriate.
  3. Individuals already funded by a MIDAS Project are ineligible for additional salary support.
  4. The project should address research topics related to the University of Pittsburgh MIDAS National of Excellence themes (e.g., public health dynamics, environmental influences, human behavioral changes, social networks, complex systems, systems thinking, policy, etc).
  5. All pilot investigators and research team members must meet University requirements for conducting research, including current certification for research ethics training. If you are outside of the University of Pittsburgh/UPMC system, you must provide evidence of current research certifications from your home Institution.
  6. Proposals demonstrating collaboration across two or more disciplines are a high priority.
  7. Publication of findings in peer-reviewed journals and subsequent applications for NIH-research grant funding (K awards, R03 and R01 awards, etc) are expected from the recipient(s) of a Seed Grant.

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Budget

 

Funds may not be used to cover investigator effort on Seed Grant projects. Note, however, effort is required by the principal investigator, must be reflected on the budget page, and must be cost shared by the department or other entity that will support such effort. Funds may be used to cover project supplies, or other purposes related directly to the conduct of the research. The monies awarded will support direct costs only; no indirect support will be provided.

Funds may not be requested for travel expenses. Personal computer purchase will be approved only when it can be demonstrated that the computer is essential for the exclusive use of this project. Justification must be provided for any equipment item costing more than $500. Costs that also are not allowable include dues for professional societies, subscription to journals, and major equipment (<$5K). Individuals already funded by a MIDAS Project are ineligible for additional salary support. Any salary support requested in a submitted budget should reflect institutional federal fringe benefit rates at their Institution.

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MIDAS Development Grants

Development Grant Information

  1. Development Grants are intended to permit the development of techniques or novel approaches to expand the field of computational modeling and simulation of infectious diseases by engaging new investigators from various academic backgrounds and training.
  2. Maximum award of $10,000 (direct costs) annually with the possibility of renewal.
  3. Eligibility is restricted to full-time junior and senior faculty, including research faculty and investigators new to computational modeling and simulation of infectious diseases.
  4. Consideration for a planned collaboration with an investigator affiliated with the Pittsburgh MIDAS National Center of Excellence would be viewed favorably but not required.
  5. A letter of support from the Principal Investigator affiliated/associated with the University of Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network is required if the applicant is outside of the University of Pittsburgh/UPMC system.

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Eligibility

  1. The Principal Investigator is required to be a full-time faculty member of any rank from any school, department, or center at the University of Pittsburgh, UPMC, RUPHI, affiliated Institution associated with the University of Pittsburgh MIDAS National Center of Excellence and/or MIDAS National Network.
  2. Individuals already funded by a MIDAS Project are ineligible for additional salary support.
  3. The project should address research topics related to the University of Pittsburgh MIDAS National of Excellence themes (e.g., public health dynamics, environmental influences, human behavioral changes, social networks, complex systems, systems thinking, policy, etc).
  4. All pilot investigators and research team members must meet University requirements for conducting research, including current certification for research ethics training. If you are outside of the University of Pittsburgh/UPMC system, you must provide evidence of current research certifications from your home Institution.
  5. Proposals demonstrating collaboration between investigators from two or more disciplines are a priority.
  6. Publication of findings in peer-reviewed journals and applications for NIH-research grant funding (K awards, R03 and R01 awards, etc) are expected from recipient(s) of a Development Grant.

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Budget

Funds may be used to cover investigator effort on Development Grants. However, effort is required by the principal investigator, must be reflected on the budget page, and must be cost shared equally by the department or other entity that will support such effort. Funds may be used to cover supplies, or other purposes related directly to the conduct of the research. The monies awarded will support direct costs only; no indirect support will be provided.

Funds may not be requested for travel expenses. Personal computer purchase will be approved only when it can be demonstrated that the computer is essential for the exclusive use of this research project. Justification must be provided for any equipment item costing more than $500. Costs that also are not allowable include dues for professional societies, subscription to journals, and major equipment (<$5K). Individuals already funded by a MIDAS Project are ineligible for additional salary support. Any salary support requested in a submitted budget should reflect federal fringe benefit rates at their Institution.

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Application Process:

The application for the Pilot Research Grant Program must contain the following:

  1. A cover letter detailing the type of award requested (Seed Grant or Development Grant). The cover page should include the title of the proposed project and the name, degree, academic title, primary department affiliation and contact information (telephone number, fax number and email address) of the Principal Investigator.
  2. A 1-page abstract summarizing the study goals, design, methods (not to exceed 250 words) and expected outcomes.
  3. NIH Biographical Sketches and Other Support information are required for the Principal Investigator and all other participants.
  4. A description of the pilot project, including specific aims, innovation, approach and significance (not to exceed 4 pages).
  5. A description of how the preliminary data, if successfully obtained, will be used in a grant application in the future, including a description of the overall aims and a broad overview of the methods of the future grant proposal (not to exceed 1-page).
  6. A description outlining the collaborators multidisciplinary research and discipline (not to exceed a ½ page).
  7. A letter of support from postdoctoral applicant’s current research faculty member (applies to Seed Grants only).
  8. A letter of support from the Principal Investigator affiliated/associated with University of Pittsburgh MIDAS National Center of Excellence and/or the MIDAS National Network (applies to Developmental Grants if applicant is outside of the University of Pittsburgh/UPMC system).
  9. A budget and budget justification (not to exceed 2 pages).
  10. Copy of Certification for required documents (Conflict of Interest, Research Integrity – internal applicants only). If outside the of the University of Pittsburgh/UPMC system, a copy of current research certifications/training will be needed.
  11. A departmental account number will be required for cost sharing purposes for internal applicants. A letter outlining the cost sharing proposal will be needed for external applicants.

The application must be clear, readily legible and conform to the following three requirements: 1) the font must be 11-point; 2) margins, in all directions, must be at least ½ inch; 3) text in figures, charts, tables, figure legends, and footnotes may be smaller in size but must be in black ink and readily legible. If these are not legible, there may be a negative impact on the evaluation of the application. Adherence to type size and line spacing requirements is necessary for several reasons. No applicant should have the advantage, by using small type, of providing more text in his or her application. Small type may also make it difficult for reviewers to read the application.

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Resources:

One of the goals of the pilot research grant program is to help investigators new to the area obtain experience in computational modeling and simulation of infectious disease. Therefore, the Public Health Dynamics laboratory at the University of Pittsburgh is available to serve as a resource for pilot awardees in developing interdisciplinary approaches using computational models to improve the understanding of theory and practice of complex issues that arise in public health (www.phdl.pitt.edu).

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Review Considerations:

The University of Pittsburgh MIDAS National Center of Excellence Pilot Grant Review Committee will review applications based on the criteria listed below:

  1. Responsiveness to the request for applications
  2. Standard NIH research criteria: significance, approach, innovation, research environment, applicant, collaborators
  3. Potential for future independent funding
  4. Feasibility within cost and time constraints
  5. Multidisciplinary collaboration with a MIDAS research project.
  6. Value to the University of Pittsburgh MIDAS National Center of Excellence.

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    Submission, Review and Award:

    Applications are to be submitted electronically in pdf format to the MIDAS Education & Outreach Coordinator, Dr. Phillip Palmer (This email address is being protected from spambots. You need JavaScript enabled to view it.). Dr. Palmer will send an e-mail message acknowledging receipt of the electronic application within one week of submission. Investigators should contact Dr. Palmer if this messages is not received.

    Applications must be received by 11:59 pm (EST) on April 16, 2012.

    Applications will be reviewed by the Pilot Research Grant Review Committee. The recommendations of this committee will be carefully considered by the University of Pittsburgh MIDAS National Center of Excellence leadership in determining which applications will receive awards. All final decisions regarding the awards are subject to the approval of the Principal Investigator of the University of Pittsburgh MIDAS National Center of Excellence, Dr. Donald S. Burke.

    All budget items must be explicitly justified. As noted, applications involving junior investigators or investigators who are seeking to integrate modeling and simulation into their research programs are of high priority.

    It is anticipated that 2 Seed Grants and 4 Development Grants will be awarded.

    RFA Release Date: January 18, 2012

    Proposal Due Date: April 16, 2012

    Project Start Date: September 1, 2012

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    Obligation of awardees:

    The MIDAS Pilot Grants have been established as 12 month awards. Awardees must complete expenditures by June 30, 2013. The Principal Investigator is expected to provide a written progress report every 6 months during the period of the award. These biannual progress reports are similar in format to an NIH progress report, listing the specific aims and any deviations from them, results, publications and any related or follow-up applications or awards for funding. All awardees must inform the MIDAS Project Coordinator, Ms. Katie Philp (This email address is being protected from spambots. You need JavaScript enabled to view it.), of any publications that arise from this funding source and acknowledge the NIGMS MIDAS Grant 5U54GM088491. Any requests for revision of aims or budget during the course of the project should be sent in writing to the Director of the MIDAS Education & Outreach Core: Dr. Joan M. Lakoski (This email address is being protected from spambots. You need JavaScript enabled to view it.).

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    Questions Regarding the Program:

    Scientific and other questions can be addressed to the Director of the MIDAS Education & Outreach Core: Dr. Joan M. Lakoski (This email address is being protected from spambots. You need JavaScript enabled to view it.) or the MIDAS Education & Outreach Coordinator: Dr. Phillip Palmer (This email address is being protected from spambots. You need JavaScript enabled to view it.), Suite M-252A Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, Phone: (412) 648-9572, Fax: (412) 624-3858.

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