Epidemiology

Cyclosporiapsis Outbreak in Texas 2017

You can find the code for this post at Cyclosporiasis is an intestinal sickness caused by the coccidian parasite Cyclospora cayetanensis. An outbreak in 2017 seemingly from Mexican cilantro has affected many people, and the Texas public health board and CDC put out some of the data publically. I wanted to go through this data, make choropleth plots for the counties affected (because I am unfamiliar with Texan counties) and plot out the data.

Summary measures of predictive power associated with logistic regression models of disease risk

For an ordinary least squares regression model, the coefficient of determination R2 describes the proportion (or percentage) of variance of the response variable explained by the model, and is a widely-accepted summary measure of predictive power. A …

Network analysis: a systems framework to address grand challenges in plant pathology

Plant pathology must address a number of challenges, most of which are characterized by complexity. Network analysis offers useful tools for addressing complex systems and an opportunity for synthesis within plant pathology and between it and …

A framework for optimizing phytosanitary thresholds in seed systems

Seedborne pathogens and pests limit production in many agricultural systems. Quarantine programs help reduce the introduction of exotic pathogens into a country, but few regulations directly apply to reducing the re-introduction and spread of …

Temperature and light effects on germination of Peronospora effusa sporangia

Spinach downy mildew, caused by the biotrophic oomycete *Peronospora effusa*, is an economically important disease that is found in all spinach growing regions of the US. To effectively predict disease risk we need to understand the response of *P. …

Laurel wilt in natural and agricultural ecosystems: understanding the drivers and scales of complex pathosystems

Laurel wilt kills members of the Lauraceae plant family in the southeastern United States. It is caused by *Raffaelea lauricola* T.C. Harr., Fraedrich and Aghayeva, a nutritional fungal symbiont of an invasive Asian ambrosia beetle, *Xyleborus …

Spatiotemporal patterns in the airborne dispersal of spinach downy mildew

Downy mildew is the most devastating disease threatening sustainable spinach production, particularly in the organic sector. The disease is caused by the biotrophic oomycete pathogen *Peronospora effusa*, and the disease results in yellow lesions …

Season-long dynamics of spinach downy mildew determined by spore trapping and disease incidence

*Peronospora effusa* is an obligate oomycete that causes downy mildew of spinach. Downy mildew threatens sustainable production of fresh market organic spinach in California, and routine fungicide sprays are often necessary for conventional …

First report of Cytospora punicae causing wood canker and branch dieback of pomegranate (Punica granatum) in the United States

Pomegranates (*Punica granatum* L.) are an expanding industry in the United States with California growing approximately 32,000 acres with a crop value of over $155 million (1). During June and July of 2012, we observed severe limb and branch dieback …

First report of Diplodia seriata causing pear branch canker dieback in California

California produces 26% of the United States pear crop on approximately 5,600 ha. A survey of seven northern California pear orchards (Pyrus communis cv. Bartlett) in summer 2010 revealed the presence of wedge-shaped cankers on 2- to 5-cm diameter …