Bayes Theorem

Australian spiny mountain crayfish (Euastacus, Parastacidae) and their ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes) may have co-occurred and interacted through deep time, during a period of major environmental change. Therefore, reconstructing the history of their association is of evolutionary, ecological, and conservation significance. Here, time-calibrated Bayesian phylogenies of Euastacus species and their temnocephalans (Temnohaswellia and Temnosewellia) indicate near-synchronous diversifications from the Cretaceous. Statistically significant cophylogeny correlations between associated clades suggest linked evolutionary histories. However, there is a stronger signal of codivergence and greater host specificity in Temnosewellia, which co-occurs with Euastacus across its range. Phylogeography and analyses of evolutionary distinctiveness (ED) suggest that regional differences in the impact of climate warming and drying had major effects both on crayfish...

Fasciolid flukes are among the largest and best known digenetic trematodes and have considerable historical and veterinary significance. Fasciola hepatica is commonly implicated in causing disease in humans. The origins, patterns of diversification, and biogeography of fasciolids are all ...

When making choices, individuals can follow alternative strategies or decision rules to the traditional compensatory utility maximization, raising doubts about to what extent these choices can be used to elicit preferences. In this paper we use a verbal protocol approach to investigate the use of alternative decision rules in discrete choice experiments. The main interest is to identify some of

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatel...

Limonium narbonense Miller is a fertile tetraploid species with a sporophytic self-incompatibility system. This sea lavender is found in coastal salt marshes which have been under intense human pressure during the past decades resulting in significant habitat fragmentation. Eleven microsatellite loci specifically designed for this species were amplified in 135 individuals from five populations. These markers were used to investigate the polyploid nature, the levels of genetic diversity and population structure in this species. L. narbonense showed high levels of genetic diversity (A = 7.82, P = 100% H T = 0.446), consistent with its likely autotetraploid origin revealed in this study and obligate outcrossing breeding system. Inbreeding (F IS) values were low in the three southern populations (mean F IS = 0.062), and higher in the northern populations (mean F IS = 0.184). Bayesian analysis of population structure revealed that populations could be grouped into two genetic clusters, one including three southern populations and the other the two northernmost ones. Individuals from the two northernmost populations showed higher admixture of the two genetic clusters than individuals from the three southern ones. A thorough analysis of microsatellite electrophoretic patterns suggests an autotetraploid origin for L. narbonense. The genetic structure revealed in this study is attributed to a recent migration from the southern area. This result suggests a net gene flow from the south to the north, likely facilitated by migratory movements of birds visiting the temporary flooded ponds occupied by L. narbonense.

Knowledge about current patterns of genetic structure of populations together with the evolutionary history of a species helps to understand and predict the adaptation of populations to future climate change. We assayed variation at nuclear microsatellite markers among peripheral vs. continuous populations of the temperate South American species Austrocedrus chilensis, to investigate the role of historical vs. demographical forces in shaping population genetic structure. This species occurs in continuous populations in the west and central distribution range, but becomes highly fragmented at the eastern limit, which comprised ice-free areas during Quaternary glaciations and has extreme climatic conditions at present times. Bayesian analysis methods identified two contrasting patterns of genetic structure; (I) populations from humid, mesic and peri-glacial regions formed a single deme with relatively low genetic differentiation and high admixture levels whereas (II) a highly heterogeneous genetic structure with low level of admixture was found in the steppe, towards the east and northeast limit of the distribution range. In the steppe, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. In addition, several small steppe populations showed high genetic diversity and divergent gene pools, suggesting that they constitute ancient refuges from pre-Holocene glaciations with just a subgroup of them contributing significantly to post-glacial spread. These results are discussed in relation to patterns of genetic variation found for other temperate species and the contribution of the particular southern Andes topography and climate to post-glacial spread.

This paper describes a Bayesian model for the assessment of inhalation exposures in an occupational setting; the methodology underpins a freely available web-based application for exposure assessment, the Advanced REACH Tool (ART). The ART is a higher tier exposure tool that combines disparate sources of information within a Bayesian statistical framework. The information is obtained from expert knowledge expressed in a calibrated mechanistic model of exposure assessment, data on inter- and intra-individual variability in exposures from the literature, and context-specific exposure measurements. The ART provides central estimates and credible intervals for different percentiles of the exposure distribution, for full-shift and long-term average exposures. The ART can produce exposure estimates in the absence of measurements, but the precision of the estimates improves as more data become available. The methodology presented in this paper is able to utilize partially analogous data, a...

ACADEMIC EMERGENCY MEDICINE 2012; 19:139–146 © 2012 by the Society for Academic Emergency MedicineACADEMIC EMERGENCY MEDICINE 2012; 19:139–146 © 2012 by the Society for Academic Emergency MedicineAbstractObjectives:  The objective was to identify high-risk census tracts, defined as those areas that have both a high incidence of out-of-hospital cardiac arrest (OHCA) and a low prevalence of bystander cardiopulmonary resuscitation (CPR), by using three spatial statistical methods.Methods:  This was a secondary analysis of two prospectively collected registries in the city of Columbus, Ohio. Consecutive adult (≥18 years) OHCA patients, restricted to those of cardiac etiology and treated by emergency medical services (EMS) from April 1, 2004, to April 30, 2009, were studied. Three different spatial analysis methods (Global Empirical Bayes, Local Moran’s I, and SaTScan’s spatial scan statistic) were used to identify high-risk census tracts.Results:  A total of 4,553 arrests in 200 census tracts occurred during the study period, with 1,632 arrests included in the final sample after exclusions for no resuscitation attempt, noncardiac etiology, etc. The overall incidence for OHCA was 0.70 per 1,000 people for the 6-year study period (SD = ±0.52). Bystander CPR occurred in 20.2% (n = 329), with 10.0% (n = 167) surviving to hospital discharge. Five high-risk census tracts were identified by all three analytic methods.Conclusions:  The five high-risk census tracts identified may be possible sites for high-yield targeted community-based interventions to improve CPR training and cardiovascular disease education efforts and ultimately improve survival from OHCA.Objectives:  The objective was to identify high-risk census tracts, defined as those areas that have both a high incidence of out-of-hospital cardiac arrest (OHCA) and a low prevalence of bystander cardiopulmonary resuscitation (CPR), by using three spatial statistical methods.Methods:  This was a secondary analysis of two prospectively collected registries in the city of Columbus, Ohio. Consecutive adult (≥18 years) OHCA patients, restricted to those of cardiac etiology and treated by emergency medical services (EMS) from April 1, 2004, to April 30, 2009, were studied. Three different spatial analysis methods (Global Empirical Bayes, Local Moran’s I, and SaTScan’s spatial scan statistic) were used to identify high-risk census tracts.Results:  A total of 4,553 arrests in 200 census tracts occurred during the study period, with 1,632 arrests included in the final sample after exclusions for no resuscitation attempt, noncardiac etiology, etc. The overall incidence for OHCA was 0.70 per 1,000 people for the 6-year study period (SD = ±0.52). Bystander CPR occurred in 20.2% (n = 329), with 10.0% (n = 167) surviving to hospital discharge. Five high-risk census tracts were identified by all three analytic methods.Conclusions:  The five high-risk census tracts identified may be possible sites for high-yield targeted community-based interventions to improve CPR training and cardiovascular disease education efforts and ultimately improve survival from OHCA.

The prefrontal cortex (PFC) subserves reasoning in the service of adaptive behavior. Little is known, however, about the architecture of reasoning processes in the PFC. Using computational modeling and neuroimaging, we show here that the human PFC has two concurrent inferential tracks: (i) one from ventromedial to dorsomedial PFC regions that makes probabilistic inferences about the reliability of the ongoing behavioral strategy and arbitrates between adjusting this strategy versus exploring new ones from long-term memory, and (ii) another from polar to lateral PFC regions that makes probabilistic inferences about the reliability of two or three alternative strategies and arbitrates between exploring new strategies versus exploiting these alternative ones. The two tracks interact and, along with the striatum, realize hypothesis testing for accepting versus rejecting newly created strategies.

Bovine besnoitiosis, caused by the apicomplexan parasite Besnoitia besnoiti is considered an emergent disease in Europe. This study aimed to determine the prevalence and geographic distribution of B. besnoiti in cattle herds in continental Portugal and to identify potential spatial clustering of infection. A stratified two-stage cross-sectional serological survey was carried out between March 2012 and May 2013 with the five administrative NUTS II regions, Norte, Centro, Lisboa, Alentejo, and Algarve, as the stratification level. Sera from 391 herds in 220 parishes and 83 municipalities were analyzed by a serial testing strategy, with the modified agglutination test (B-MAT) as the first screening assay and the immunofluorescent antibody test (IFAT) as the confirmatory test. Within-herd prevalence of positive herds varied between 0.7 and 72.4% and was ≥10.3% in half of the infected herds. Using a Bayesian approach, the true prevalence of B. besnoiti in cattle herds was determined to be 5.1% (confidence interval (CI), 3.1-7.8%) and the mean within-herd prevalence of positive herds was 33.0% (CI, 20.3-46.0%). The sensitivity and specificity of the B-MAT were estimated to be 96.9% (CI, 93.7-98.8 %) and 99.7% (CI, 99.6-99.8%), whereas those of the IFAT were 89.6% (CI, 86.0-92.5%) and 99.7% (CI, 98.5-99.9%), respectively. Spatial scan statistics analysis identified one spatial cluster covering the majority of the Alentejo region. Seropositive herds were detected for the first time outside Alentejo, in the region Centro and in the northeast of Portugal. Further epidemiological research is needed to identify eco-biological factors, which could explain the geographic clustering of B. besnoiti in Portugal.

In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown-source microorganisms. Culture medium, presence of agar, culturing temperature, and drying method are just some of the broad spectrum of characteristics an investigator might like to infer. The effects of many of these factors on microorganisms are not well understood, but the complex way in which microbes interact with their environments suggests that numerous analytical techniques measuring different properties will eventually be needed for complete characterization. In this work, we present a Bayesian statistical framework for integrating disparate analytical measurements. We illustrate its application to the problem of characterizing the culture medium of Bacillus spores using three different mass spectral techniques. The results of our study suggest that integrating data in this way significantly improves the accuracy and robustness of the analyses.