An American BSE Crisis: Has it affected the Value of Traceability and Country-of-Origin Certifications for US and Canadian Beef?

With a BSE incident in the United States (US) in December of 2003, questions arose about the effect of the incident on consumers in the US. The purpose of this paper is to determine if traceability systems for beef can help preserve consumer demand following the discovery of BSE. Auctions were conducted approximately 3 weeks before and after the December 2003 BSE incident in the U.S It was found that overall there was no effect on the size of the bribes needed by the BSE incidence. However, for some groups there were important changes. The results indicate that information about traceability and country of origin is valuable to consumers. They also suggest that greater uncertainty about certifications and assurances for beef existed among the participants after December 23rd than before December 23rd.BSE, Traceability, Country-of-origin, Beef market, Auctions, Food Consumption/Nutrition/Food Safety, Livestock Production/Industries,

An Evaluation of a Battery of Functional and Structural Tests as Predictors of Likely Risk of Progression of Age-Related Macular Degeneration.

Purpose: To evaluate the ability of visual function and structural tests to identify the likely risk of progression from early/intermediate to advanced AMD, using the Age-Related Eye Disease Study (AREDS) simplified scale as a surrogate for risk of progression. The secondary aim was to determine the relationship between disease severity grade and the observed functional and structural deficits. Methods: A total of 100 participants whose AMD status varied from early to advanced were recruited. Visual function was assessed using cone dark adaptation, 14 Hz flicker and chromatic threshold tests and retinal structure was assessed by measuring drusen volume and macular thickness. The predictive value of the tests was estimated using ordinal regression analysis. Group comparisons were assessed using analysis of covariance. Results: Change in cone dark adaptation (cone τ) and yellow-blue (YB) chromatic sensitivity were independent predictors for AMD progression risk (cone τ, pseudo R2 = 0.35, P < 0.001; YB chromatic threshold, pseudo R2 = 0.16, P < 0.001). The only structural predictor was foveal thickness (R2 = 0.05, P = 0.047). Chromatic sensitivity and cone dark adaptation were also the best functional tests at distinguishing between severity groups. Drusen characteristics clearly differentiated between participants with early and advanced disease, but were not able to differentiate between those with early AMD and controls. Mean differences in retinal thickness existed between severity groups at the foveal (P = 0.040) and inner (P = 0.001) subfields. Conclusions: This study indicates that cone τ, YB chromatic threshold and foveal thickness are independent predictors of likely risk of AMD progression

Probit models for capture-recapture data subject to imperfect detection, individual heterogeneity and misidentification

As noninvasive sampling techniques for animal populations have become more popular, there has been increasing interest in the development of capture-recapture models that can accommodate both imperfect detection and misidentification of individuals (e.g., due to genotyping error). However, current methods do not allow for individual variation in parameters, such as detection or survival probability. Here we develop misidentification models for capture-recapture data that can simultaneously account for temporal variation, behavioral effects and individual heterogeneity in parameters. To facilitate Bayesian inference using our approach, we extend standard probit regression techniques to latent multinomial models where the dimension and zeros of the response cannot be observed. We also present a novel Metropolis-Hastings within Gibbs algorithm for fitting these models using Markov chain Monte Carlo. Using closed population abundance models for illustration, we re-visit a DNA capture-recapture population study of black bears in Michigan, USA and find evidence of misidentification due to genotyping error, as well as temporal, behavioral and individual variation in detection probability. We also estimate a salamander population of known size from laboratory experiments evaluating the effectiveness of a marking technique commonly used for amphibians and fish. Our model was able to reliably estimate the size of this population and provided evidence of individual heterogeneity in misidentification probability that is attributable to variable mark quality. Our approach is more computationally demanding than previously proposed methods, but it provides the flexibility necessary for a much broader suite of models to be explored while properly accounting for uncertainty introduced by misidentification and imperfect detection. In the absence of misidentification, our probit formulation also provides a convenient and efficient Gibbs sampler for Bayesian analysis of traditional closed population capture-recapture data.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS783 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Defect Formation and Kinetics of Atomic Terrace Merging

Pairs of atomic scale terraces on a single crystal metal surface can be made to merge controllably under suitable conditions to yield steps of double height and width. We study the effect of various physical parameters on the formation of defects in a kinetic model of step doubling. We treat this manifestly non- equilibrium problem by mapping the model onto a 1-D random sequential adsorption problem and solving this analytically. We also do simulations to check the validity of our treatment. We find that our treatment effectively captures the dynamic evolution and the final state of the surface morphology. We show that the number and nature of the defects formed is controlled by a single dimensionless parameter $q$. For $q$ close to one we show that the fraction of defects rises linearly with $\epsilon \equiv 1-q$ as $0.284 \times \epsilon$. We also show that one can arrive at the final state faster and with fewer defects by changing the parameter with time.Comment: 17 pages, 8 figures. To be submitted to Phys. Rev.

A Dual Read-Out Assay to Evaluate the Potency of Compounds Active against Mycobacterium tuberculosis

PMCID: PMC3617142This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Slow epidemic extinction in populations with heterogeneous infection rates

We explore how heterogeneity in the intensity of interactions between people affects epidemic spreading. For that, we study the susceptible-infected-susceptible model on a complex network, where a link connecting individuals $i$ and $j$ is endowed with an infection rate $\beta_{ij} = \lambda w_{ij}$ proportional to the intensity of their contact $w_{ij}$, with a distribution $P(w_{ij})$ taken from face-to-face experiments analyzed in Cattuto $et\;al.$ (PLoS ONE 5, e11596, 2010). We find an extremely slow decay of the fraction of infected individuals, for a wide range of the control parameter $\lambda$. Using a distribution of width $a$ we identify two large regions in the $a-\lambda$ space with anomalous behaviors, which are reminiscent of rare region effects (Griffiths phases) found in models with quenched disorder. We show that the slow approach to extinction is caused by isolated small groups of highly interacting individuals, which keep epidemic alive for very long times. A mean-field approximation and a percolation approach capture with very good accuracy the absorbing-active transition line for weak (small $a$) and strong (large $a$) disorder, respectively

Solution of an infection model near threshold

We study the Susceptible-Infected-Recovered model of epidemics in the vicinity of the threshold infectivity. We derive the distribution of total outbreak size in the limit of large population size $N$. This is accomplished by mapping the problem to the first passage time of a random walker subject to a drift that increases linearly with time. We recover the scaling results of Ben-Naim and Krapivsky that the effective maximal size of the outbreak scales as $N^{2/3}$, with the average scaling as $N^{1/3}$, with an explicit form for the scaling function