Investigators
Thomas E. Dick Frank J. Jacono, Kennth A. Loparo, Yoram Vodovotz, and Yaroslav Molkov
1. Define context(s)
aid in clinical decision making
reveal new biological insights
Primary goal of the model/tool/database
Our project builds on iterative interaction between modeling (data-driven and mechanistic [differential equation-based]) and experiments to determine how brainstem inflammation limits variability of physiologic patterns and uncouples biologic rhythms. Specifically, we ask do increases in the predictability of ventilatory pattern variability (VPV) and/or decreases in cardio-respiratory coupling (CRC) reflect increases in proinflammatory cytokines in the ponto-medullary circuitry controlling homeostasis. Our primary goal is to determine if quantifying VPV and CVC produce biometrics that track a health and herald the onset of sepsis. The biologic domains of the model are the expression and control of the inflammatory cytokines in the nucleus tractus solitarii, nucleus Ambiguus, and Kölliker-Fuse nuclei, which are critical nuclei in brainstem control circuits of the cardiac, sympathetic and respiratory effectors. Thus, in the experimental protocol the time scales correspond to: 1) the 10-100 milliseconds involved in the time course of cytokines effecting the synaptic efficacy in the control circuits, 2) the 0.1-1 or 1-5 seconds involved in the expression of the cardiac and respiratory cycles in rats and humans, respectively, 3) 6 - 48 hours involved in tracking the development of sepsis after systemic inoculation in rats and 4) 1-7 days in tracking critically ill patients. Currently, in the mechanistic model, we are focusing on the interaction between the autonomic and respiratory effectors, i.e., drawing scalable models for investigating the neural control of respiratory-modulation of heart rate and blood pressure and the tendency for respiratory rhythm to be delayed with increases in arterial pulse pressure. In the data-driven models of central cytokine expression, the time scales are 6-48 hours.
Biological domain of the model
Central nervous system
Structure(s) of interest in the model
Brainstem Neural Circuitry and Cytokine Networks within the Brainstem
Spatial scales included in the model
Synapses, Neurons, Central Nuclei, Circuits, and Behavior Expression
Time scales included in the model
Milliseconds, Seconds, Hours and Days
2. Data for building and validating the model
Data for building the model |
Published? |
Private? |
How is credibility checked? |
Current Conformance Level / Target Conformance Level |
in vitro (primary cells cell, lines, etc.) |
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ex vivo (excised tissues) |
Accptd 02/20 |
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Repeated in-house & consistent with previous publications |
adequate |
in vivo pre-clinical (lower-level organism or small animal) |
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In review 2 manuscripts in preparation Collecting data |
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in vivo pre-clinical (large animal) |
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Human subjects/clinical |
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Yes |
Colleague shared her data Collecting data |
extensive |
Other: ________________________ |
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Data for validating the model |
Published? |
Private? |
How is credibility checked? |
Current Conformance Level / Target Conformance Level |
in vitro (primary cells cell, lines, etc.) |
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ex vivo (excised tissues) |
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in vivo pre-clinical (lower-level organism or small animal) |
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Will plan experiments to test hypotheses of both models |
adequate |
in vivo pre-clinical (large animal) |
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Human subjects/clinical |
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Collecting data |
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partial |
Other: ________________________ |
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3. Validate within context(s)
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Who does it? |
When does it happen? |
How is it done? |
Current Conformance Level / Target Conformance Level |
Verification |
DyNA Yoram Vodovotz & Ruben Zamora; ODE Model, Yaroslav Molkov, PI; William Barnett, senior post doc; & graduate students |
DyNA, Yoram Vodovotz & Ruben Zamora; ODE Model, weekly |
DyNA, Compare models from similar but separate experimental protocols; ODE Model, Model was implemented by independent researchers in different computing environments |
adequate |
Validation |
DyNA Yoram Vodovotz & Ruben Zamora; ODE Model, Yaroslav Molkov, William Barnett |
DyNA, Spring 2021;ODE Model, Manuscript Spring 2020 |
DyNA, Compare models from a distinct protocol/perturbation suggested by the model; ODE Model, We inferred mechanisms from neuro-physiologic recordings in rats & predicted human data. |
adequate |
Uncertainty quantification |
DyNA Yoram Vodovotz & Ruben Zamora; ODE Model, Yaroslav Molkov, William Barnett |
DyNA, Spring 2021;ODE Model, Manuscript Spring 2020 |
DyNA, Reproducibility of DyNA networks at similar stringency level across separate verification scenarios;ODE Model, Comparison of model and human probability density functions for heartbeats relative to the onset of inspiration. |
adequate |
Sensitivity analysis |
DyNA Yoram Vodovotz & Ruben Zamora; ODE Model, Yaroslav Molkov, PI; William Barnett, senior post doc; & graduate students |
DyNA&ODE: Current with each model |
DyNA, Variables are excluded and variable ranges are determined; ODE Model, |
adequate |
Other:__________ |
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Additional Comments |
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4. Limitations
Disclaimer statement (explain key limitations) |
Who needs to know about this disclaimer? |
How is this disclaimer shared with that audience? |
Current Conformance Level / Target Conformance Level |
DyNA network models are based on correlations across time intervals. DyNA models are thus “quasi-dynamic” in that they represent linearized portions of a full time course, as opposed to being run on all of the data from a given time course at once. |
Consumers and Users |
Mi, Q.; Constantine, G.; Ziraldo, C.; Solovyev, A.; Torres, A.; Namas, R.; Bentley, T.; Billiar, T.R.; Zamora, R.; Puyana, J.C.; Vodovotz, Y. A dynamic view of trauma/hemorrhage-induced inflammation in mice: Principal drivers and networks. PLoS ONE. 2011.6:19424. |
extensive |
ODE Model is based on correlations but the core model has extensive history and has generated testable hypotheses. |
Consumers and Users |
Stated in publications |
extensive |
In both models, accuracy of biologic data |
Consumers and Users |
Stated in publications |
extensive |
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5. Version control
Current Conformance Level / Target Conformance Level |
adequate for both DyNA ad ODE model |
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Naming Conventions? |
Repository? |
Code Review? |
individual modeler |
DyNA Ruben Zamora & ODE Model William Barnett |
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within the lab |
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collaborators |
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6. Documentation
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Current Conformance Level / Target Conformance Level |
Code commented? |
adequate for both DyNA and ODE model |
Scope and intended use described? |
adequate for both DyNA and ODE model |
User’s guide? |
The details of the DyNA model framework have been published in: Mi, Q.; Constantine, G.; Ziraldo, C.; Solovyev, A.; Torres, A.; Namas, R.; Bentley, T.; Billiar, T.R.; Zamora, R.; Puyana, J.C.; Vodovotz, Y. A dynamic view of trauma/hemorrhage-induced inflammation in mice: Principal drivers and networks. PLoS ONE. 2011.6:19424. DyNA is a data-driven model; the code is in Matlab. |
Developer’s guide? |
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7. Dissemination
Current Conformance Level / Target Conformance Level |
adequate |
Target Audience(s): |
“Inner circle” |
Scientific community |
Public |
Simulations |
adequate |
Adequate (multiple publications) |
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Models |
adequate |
Adequate (multiple publications, Matlab code available) |
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Software |
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Adequate (multiple publications, Matlab code available) |
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Results |
adequate |
Adequate (multiple publications) |
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Implications of results |
adequate |
Adequate (multiple publications) |
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8. Independent reviews
Current Conformance Level / Target Conformance Level |
review in Spring 2021 |
Reviewer(s) name & affiliation: |
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When was review performed? |
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How was review performed and outcomes of the review? |
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9. Test competing implementations
Current Conformance Level / Target Conformance Level |
review in Spring 2021 |
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Yes or No (briefly summarize) |
Were competing implementations tested? |
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Did this lead to model refinement or improvement? |
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