Majid Bani-Yaghoub

Reproduction numbers for infections with free-living pathogens growing in the environment

The basic reproduction number ℛ0 for a compartmental disease model is often calculated by the next generation matrix (NGM) approach. When the interactions within and between disease compartments are interpreted differently, the NGM approach may lead to different ℛ0 expressions. This is demonstrated by considering a susceptible–infectious–recovered–susceptible model with free-living pathogen (FLP) growing in the environment. Although the environment could play different roles in the disease transmission process, leading to different ℛ0 expressions, there is a unique type reproduction number when control strategies are applied to the host population. All ℛ0 expressions agree on the threshold value 1 and preserve their order of magnitude. However, using data for salmonellosis and cholera, it is shown that the estimated ℛ0 values are substantially different. This study highlights the utility and limitations of reproduction numbers to accurately quantify the effects of control strategies for infections with FLPs growing in the environment.

Modeling the effect of seasonal variation in ambient temperature on the transmission dynamics of a pathogen with a free-living stage: example of Escherichia coli O157:H7 in a dairy herd.

To explore the potential role of ambient temperature on infection transmission dynamics for pathogens, we used Escherichia coli O157:H7 in a dairy herd and the surrounding farm environment as a model system. For this system, we developed a mathematical model in which a Susceptible-Infectious-Susceptible (SIS) model of infection spread through the host population is coupled with a metapopulation model of E. coli O157:H7 free-living stage in the environment allowing bacterial growth to be influenced by ambient temperature. Model results indicate that seasonal variation in ambient temperature could have a considerable impact on pathogen populations in the environment, specifically on barn surfaces and in water troughs, and consequently on the prevalence of infection in the host population. Based on model assumptions, contaminated drinking water was the most important pathway of E. coli O157:H7 transmission to cattle. Sensitivity analysis indicated that water-borne transmission is amplified during the warmer months if the amount of standing drinking water available to the cattle herd is high. This is because warmer ambient temperature favors faster pathogen replication which when combined with slower water replacement-rate due to high amount of available standing water leads to a greater pathogen load in drinking water. These results offer a possible explanation of the seasonal variation in E. coli O157:H7 prevalence in cattle and suggest that improved drinking-water management could be used for control of this infection in cattle. Our study demonstrates how consideration of ambient temperature in transmission cycles of pathogens able to survive and grow in the environment outside the host could offer novel perspectives on the spread and control of infections caused by such pathogens.

Identifying areas of high risk of human exposure to coccidioidomycosis in Texas using serology data from dogs.

Coccidioidomycosis or Valley Fever (VF) is an emerging soil‐borne fungal zoonosis affecting humans and animals. Most non‐human cases of VF are found in dogs, which we hypothesize may serve as sentinels for estimating the human exposure risk. The objective of this study is to use the spatial and temporal distribution and clusters of dogs seropositive for VF to define the geographic area in Texas where VF is endemic, and thus presents a higher risk of exposure to humans. The included specimens were seropositive dogs tested at a major diagnostic laboratory between 1999 and 2009. Data were aggregated by zip code and smoothed by empirical Bayesian estimation to develop an isopleth map of VF seropositive rates using kriging. Clusters of seropositive dogs were identified using the spatial scan test. Both the isopleth map and the scan test identified an area with a high rate of VF‐seropositive dogs in the western and southwestern parts of Texas (relative risk = 31). This location overlapped an area that was previously identified as a potential endemic region based on human surveys. Together, these data suggest that dogs may serve as sentinels for estimating the risk of human exposure to VF.

Effectiveness of environmental decontamination as an infection control measure.

The effectiveness of environmental decontamination (ED) as a measure in the control of infectious diseases is controversial. This work quantifies the effectiveness of ED by analysing the transmission of pathogens from the environment to susceptible hosts in a Susceptible-Infected-Susceptible model. Analysis of the model shows that ED can render a population disease-free only when the duration of infection (D) is within a certain range. As host-to-host transmission rate is increased, D falls outside this range and the higher levels of ED have a diminishing return in reducing the number of infected hosts at endemic equilibrium. To avoid this, ED can be combined with other control measures, such as treating infected individuals to push the duration of infection into the specified range. We propose decision criteria and minimum ED efforts required for control policies to be effective.

Understanding the role of cleaning in the control of Salmonella Typhimurium in grower-finisher pigs: a modelling approach.

Salmonella Typhimurium (STM) infection in pigs represents a considerable food safety concern. This study used mathematical modelling to evaluate the effectiveness of cleaning (faeces removal) as a measure to control STM spread among grower-finisher pigs. A modified Susceptible-Infected-Recovered-Susceptible (SIRS) model of STM transmission through a contaminated environment was developed. Infected pigs were divided into three states according to the pathogen level being shed in their faeces. Infection transmission was evaluated using the basic reproduction number (R 0) and the prevalence of infectious pigs at slaughter age. Although increased frequency and efficiency of cleaning did reduce the prevalence of STM shedding at the time of slaughter, these efforts alone were not capable of eliminating the infection from the population. The level of STM faecal shedding by infectious pigs strongly influenced the infection spread and prevalence at slaughter. To control STM in pigs, cleaning should be combined with vaccination and/or isolation of high-level shedders.

Existence and stability of stationary waves of a population model with strong Allee effect

We investigate the existence and stability of stationary waves of a nonlocal reaction-diffusion population model with delay, nonlocality and strong Allee effect. By reducing the model, the conditions for existence of stationary wavefront, wave pulse and inverted wave pulse are established. Then we show that the stationary waves of the reduced model are also the stationary waves of the general model. The global stability of the stationary waves is illustrated by numerically solving the general model for different sets of parameter values.

Dynamics of Notch Activity in a Model of Interacting Signaling Pathways

Networks of interacting signaling pathways are formulated with systems of reaction-diffusion (RD) equations. We show that weak interactions between signaling pathways have negligible effects on formation of spatial patterns of signaling molecules. In particular, a weak interaction between Retinoic Acid (RA) and Notch signaling pathways does not change dynamics of Notch activity in the spatial domain. Conversely, large interactions of signaling pathways can influence effects of each signaling pathway. When the RD system is largely perturbed by RA-Notch interactions, new spatial patterns of Notch activity are obtained. Moreover, analysis of the perturbed Homogeneous System (HS) indicates that the system admits bifurcating periodic orbits near a Hopf bifurcation point. Starting from a neighborhood of the Hopf bifurcation, oscillatory standing waves of Notch activity are numerically observed. This is of particular interest since recent laboratory experiments confirm oscillatory dynamics of Notch activity.

Study and simulation of reaction-diffusion systems affected by interacting signaling pathways.

Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and on the process of axon formation. This can be observed by the numerical study of the homogeneous system showing that in the absence of RA–Notch interaction the unperturbed homogeneous system may exhibit different saddle-node bifurcations that are robust under small perturbations by low levels of RA–Notch interactions, while large increases in the level of RA–Notch interaction result in a number of transitions of saddle-node bifurcations into Hopf bifurcations. It is speculated that near a Hopf bifurcation, the regulations between the positive and negative feedbacks change in such a way that spontaneous symmetry breaking takes place only when transport of activated Notch protein takes place at a faster rate.

A Time Series Modeling Approach in Risk Appraisal of Violent and Sexual Recidivism

For over half a century, various clinical and actuarial methods have been employed to assess the likelihood of violent recidivism. Yet there is a need for new methods that can improve the accuracy of recidivism predictions. This study proposes a new time series modeling approach that generates high levels of predictive accuracy over short and long periods of time. The proposed approach outperformed two widely used actuarial instruments (i.e., the Violence Risk Appraisal Guide and the Sex Offender Risk Appraisal Guide). Furthermore, analysis of temporal risk variations based on specific time series models can add valuable information into risk assessment and management of violent offenders.

A nested compartmental model to assess the efficacy of paratuberculosis control measures on U.S. dairy farms

Paratuberculosis, also known as Johnes disease (JD), is a chronic contagious disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The disease is incurable, fatal and causes economic losses estimated to exceed 200 million dollars to the U.S. dairy industry annually. Several preventive and control measures have been recommended; however, only a few of these measures have been validated empirically. Using a nested compartmental (NC) modeling approach, the main objective of this research was to identify the best combination of control and preventive measures that minimizes the prevalence and incidence of JD and the risk of MAP occurrence in a dairy herd. The NC model employs both MAP transmission estimates and data on pen movement of cattle on a dairy to quantify the effectiveness of control and preventive measures. To obtain reasonable ranges of parameter values for between-pen movements, the NC model was fitted to the movement data of four typical California dairy farms. Using the estimated ranges of the movement parameters and those of JD from previous research, the basic reproduction number was calculated to measure the risk of MAP occurrence in each pen environment as well as the entire dairy. Although the interventions evaluated by the NC model were shown to reduce the infection, no single measure alone was capable of eradicating the infection. The numerical simulations suggest that a combination of test and cull with more frequent manure removal is the most effective method in reducing incidence, prevalence and the risk of MAP occurrence. Other control measures such as limiting calf-adult cow contacts, raising calves in a disease-free herd or colostrum management were less effective.