Effects of imperfect testing on presence-absence sampling plans

Sampling inspection plans are used in the food industry to determine whether a batch of food is contaminated or not. Testing for pathogens is mandatory in several foodstuffs because some bacteria pose a significant risk to human health, even when these are consumed in minute quantity. Test performance measures such as sensitivity and specificity are generally ignored in microbiological risk assessment and food quality assurance. In this research, we examine the impact of imperfect analytical tests on sampling inspection plans for presence-absence characteristics. We discuss several plausible scenarios and assess the risk for the consumers. The method is illustrated using data collected over 2 years for Cronobacter spp (formerly Enterobacter sakazakii) in skimmed milk powder. The probability of contamination and the test sensitivity and specificity are estimated using Bayesian methods. We examine the sampling plans proposed by the Codex Alimentarius and by the New Zealand's Ministry of Primary Industries for this pathogen. A cost analysis is performed to show the economic loss due to measurement errors. We describe the strengths and limitations of these plans under different conditions and propose a plan that could provide better protection to the consumers as well as to the producers.</p

A reference genome for common bean and genome-wide analysis of dual domestications

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement

Cortico-Basal Ganglia Reward Network: Microcircuitry

Many of the brain's reward systems converge on the nucleus accumbens, a region richly innervated by excitatory, inhibitory, and modulatory afferents representing the circuitry necessary for selecting adaptive motivated behaviors. The ventral subiculum of the hippocampus provides contextual and spatial information, the basolateral amygdala conveys affective influence, and the prefrontal cortex provides an integrative impact on goal-directed behavior. The balance of these afferents is under the modulatory influence of dopamine neurons in the ventral tegmental area. This midbrain region receives its own complex mix of excitatory and inhibitory inputs, some of which have only recently been identified. Such afferent regulation positions the dopamine system to bias goal-directed behavior based on internal drives and environmental contingencies. Conditions that result in reward promote phasic dopamine release, which serves to maintain ongoing behavior by selectively potentiating ventral subicular drive to the accumbens. Behaviors that fail to produce an expected reward decrease dopamine transmission, which favors prefrontal cortical-driven switching to new behavioral strategies. As such, the limbic reward system is designed to optimize action plans for maximizing reward outcomes. This system can be commandeered by drugs of abuse or psychiatric disorders, resulting in inappropriate behaviors that sustain failed reward strategies. A fuller appreciation of the circuitry interconnecting the nucleus accumbens and ventral tegmental area should serve to advance discovery of new treatment options for these conditions