Research

Mathematical and Statistical Modeling of Mycobacterial Diseases

(funded by NIH (ORIP) #8K01OD01968)

[leprosy model]

This is a model for leprosy.


Mycobacterial diseases are common to humans and animals – tuberculosis (human and cattle), leprosy, paratuberculosis – and all express similar dynamics. For instance, all have long latent periods, all are difficult to diagnose in early stages, and all are subject to extreme variations in susceptibility (ranging from full resistance through non-progressing infections to clinical disease). Our work aims to apply techniques and biological understanding gained in each disease across all mycobacterial diseases to improve our understanding of mycobacterial disease dynamics and how to control them.
In collaboration with Mycobacterial Transmission Dynamics in Agricultural Systems: Integrating Phylogenetics, Epidemiology, Ecology, and Economics (USDA:NIFA #2014-67015-2240).

Publications:

  • The effects of progressing and non-progressing Mycobacterium avium subsp. paratuberculosis infection on milk production in dairy cows. Smith, R. L.; Gröhn, Y. T.; Pradhan, A. K.; Whitlock, R. H.; Van Kessel, J. S.; Smith, J. M.; Wolfgang, D. R.; Schukken, Y. H. J. Dairy Sci. 2016 99:1383-1390. Editor’s Choice selection.
  • A new compartmental model of Mycobacterium avium subsp. paratuberculosis infection dynamics in cattle. Smith, R. L.; Gröhn, Y. T.; Schukken, Y. H. Prev. Vet. Med. 2015 122:298-305.
  • Minimum cost to control bovine tuberculosis in cow-calf herds. Smith, R. L.; Tauer, L. W.; Schukken, Y. H.; Lu, Z.; Gröhn, Y. T. Prev. Vet. Med. 2014 115:18-28.
  • Use of Approximate Bayesian Computation to assess and fit models of Mycobacterium leprae to predict outcomes of the Brazilian control program. Smith, R.L.; Grohn, Y.T. PLoS One 2015 10(6):e0129535
  • Modeling of Mycobacterium Avium Subsp. Paratuberculosis Dynamics in a Dairy Herd: An Individual Based Approach. Al-Mamun, M.; Smith, R.L.; Schukken, Y.H.; Grohn, Y.T. Journal of Theoretical Biology 2016 408:105-117.
  • Proposing a Compartmental Model for Leprosy and Parameterizing Using Regional Incidence in Brazil. Smith, R.L. PLoS Neglected Tropical Diseases 2016 10(8): e0004925.
  • Economic consequences of paratuberculosis in dairy cattle: a modeling study. Smith, R.L.; Al-Mamun, M.; Grohn, Y.T. Prev Vet Med 2017 138:17-27.


Comprehensive Modeling of Perimenopausal Health Outcomes


Up to 85% of women experience some form of symptoms associated with the menopausal transition. Our goal with this research is to better understand the underlying mechanism of these symptoms and the factors affecting their dynamics, with the ultimate goal of providing clinicians with technological tools to improve informed decision-making during mid-life.

Survival curves for Duration of Hot Flashes

Survival curves for Duration of Hot Flashes

In collaboration with Jodi Flaws and the Mid-Life Women’s Health Study (NIH (NIA) #R01 AG18400)

Publications:

  • Does quitting smoking decrease the risk of midlife hot flashes? A longitudinal analysis. Smith, R. L.; Flaws, J. A.; Gallicchio, L. Maturitas 2015 82:123-127.
  • Risk factors for extended duration and timing of peak severity of hot flashes. Smith, R.L.; Gallicchio, L.; Miller, S.R.; Zacur, H.A.; Flaws, J.A. PLoS ONE 11(5): e0155079.
  • Age at menarche, androgen concentrations, and midlife obesity: Findings from the Midlife Women’s Health Study. Gallicchio, L.; Flaws, J.A.; Smith, R.L. Menopause 2016 23(11):1182-1188.
  • Factors Affecting Sexual Activity in Mid-life Women: Results from the Midlife Health Study. Smith, R.L.; Gallicchio, L.; Flaws, J.A. Journal of Women’s Health 2017 26(2):103-108.
  • Factors Affecting Sexual Function in Mid-life Women: Results from the Midlife Health Study. Smith, R.L.; Gallicchio, L.; Flaws, J.A. Journal of Women’s Health 2017: accepted.
  • Bayesian Networks for Hot Flashes: A Multivariate Approach. Smith, R.L. et al., In review.

 


Determining the Paths of Disease Spread in Livestock


Livestock diseases spread between herds through a variety of routes: animal movements, fomites, farm visits, wildlife, etc. Our goal is to identify and quantify the impact of these different routes on the spread of disease between livestock herds. The ultimate goal is to identify the best strategies for stopping disease spread.

Publications:

  • A new perspective on fomites spread among livestock systems: from visits to contacts, and back.  Rossi, G. et al.  Scientific Reports 7:2375
  • Causes of periodicity in Orf transmission in domestic sheep flocks.  Burson, H.; Smith, R.L.  In preparation


Causes of Heterogeneity in Breast Cancer Treatment Response

ROC curve for 5 year recurrence of breast cancer after tamoxifen, based on gene expression values

ROC curve for 5 year recurrence of breast cancer after tamoxifen, based on gene expression values

Breast cancer is a highly variable disease, with many tumors failing to respond to treatments that are generally effective. Our goal is to identify the mechanism causing heterogeneous responses, both to better predict survival outcomes and to identify potential targets for new treatments.

primary collaborator: Zeynep Madak-Erdogan

Publications:

  • XPO1 regulates tamoxifen responsiveness in estrogen receptor positive breast tumors by decreasing nuclear localization of ERK5. Wrobel, K.; Zhao, Y.C.; Kulkoyluoglu, E.; Chen, K.L.A.; Hieronymi, K.; Holloway, J.; Li, S.; Ray, T.; Ray, P.S.; Lipka, A.E.; Smith, R.L.; Madak-Erdogan, Z. Molecular Endocrinology 2016 30(10):1029-1045.

 



Optimization of Multi-Disease Individual-Based Models to Improve Infectious Disease Management

(funded by NCSA Faculty Fellows Program)

more info
Farmers make disease control decisions in a multi-pathogen environment, but most disease modeling focuses only on individual pathogens. This is especially important economically, as the money available to control disease is limited and some actions (i.e., calf hygiene improvements) will be effective for multiple diseases. The goal of this project is to economically optimize disease control programs in dairy herds with multiple endemic diseases. The ultimate goal is to provide farmers with personalized decision support for disease control planning.

Other projects within this focus include the modeling of antimicrobial resistance gene transmission in different populations, including swine farms and within cystic fibrosis patients.


Risks Associated with Irrigation with Reused Water

Risk of pathogen transfer from water to plants, plants to produce, and produce to human infection

Risk of pathogen transfer from water to plants, plants to produce, and produce to human infection

As water resources become more limited with higher demand, reused water (wastewater, stormwater, and rainwater) will become more desirable for irrigation. However, this reused water could contain pathogens that risk the health of both farmers and consumers. The goal of this research is to quantify that risk and identify the most effective water treatment methods for different irrigation systems.

primary collaborator: Helen Nguyen

Publications:

  • Rotavirus infection risk after irrigation and vegetable sanitation. Fuzuwa, M. et al. In preparation
  • Risk assessment of Legionella pneumophila infection by the release from biofilms in premise plumbing. Huang, C. et al. In preparation

 

 


Infection Genomics for One Health

Microbiome research frequently focuses on individual host species. We aim to use a comparative approach to microbiome research, with the goal of better understanding the role of the microbiome in health of all hosts. Our ultimate goal is to find ways to manipulate the microbiome within hosts to improve health at the human-animal-plant-environment interface.

As part of the Woese Institute for Genomic Biology 

Theme Page: IGOH

Theme Leader: Rachel Whitaker

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