Molecular characterization and phylogenetic analysis of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC and parE gene loci in viridans group streptococci isolated from adult patients with cystic fibrosis

This study demonstrated key resistance genes to fluroquinilones in Streptococcci isolated from sputum of people with CF. This suggests that other bacteria which are sometimes considered commensal may be a resovoir for resistance. Jse designed the study with Moore.

Unconscious Vigilance: Worldview Defense without Adaptations for Terror, Coalition or Uncertainty Management

Individuals subtly reminded of death, coalitional challenges, or feelings of uncertainty display exaggerated preferences for affirmations and against criticisms of their cultural in-groups. Terror management, coalitional psychology, and uncertainty management theories postulate this “worldview defense” effectas the output of mechanisms evolved either to allay the fear of death, foster social support, or reduce anxiety by increasing adherence to cultural values. In 4 studies, we report evidence for an alternative perspective. We argue that worldview defense owes to unconscious vigilance, a state of accentuatedreactivity to affective targets (which need not relate to cultural worldviews) that follows detection of subtle alarm cues (which need not pertain to death, coalitional challenges, or uncertainty). In Studies 1 and 2, death-primed participants produced exaggerated ratings of worldview-neutral affective targets. In Studies 3 and 4, subliminal threat manipulations unrelated to death, coalitional challenges, or uncertaintyevoked worldview defense. These results are discussed as they inform evolutionary interpretations of worldview defense and future investigations of the influence of unconscious alarm on judgment.

TheShifting Sands of Uncertainty: Risk Construction and BSE/vCJD

It is more than a decade since scientists in the UK put forward evidence of a link between the emergence of a new variant of Creutzfeldt-Jakob Disease (vCJD) in humans, and a diminishing epidemic of Bovine Spongiform Encephalopathy, or BSE, in cattle. In the wake of this anniversary, the paper revisits two scientific narratives of risk, forged at different points along the developmental pathway of BSE science, including a series of advisory reports provided to the UK government between 1989 and 1994, and a symposium held in 2001 to assess the impact of the Phillips Inquiry. While the primary pathology of BSE became apparent relatively early on, uncertainties remain about the origins of BSE and its human variant, vCJD. The paper examines the handling of this sensitivity, and its communication, within these key documents, noting changes in patterns of uncertainty construction over time.

Chernobyl: Living with Risk and Uncertainty

The nuclear accident in Chernobyl in 1986 is a dramatic example of the type of incidents that are characteristic of a risk society. The consequences of the incident are indeterminate, the causes complex and future developments unpredictable. Nothing can compensate for its effects and it affects a broad population indiscriminately. This paper examines the lived experience of those who experienced biographical disruption as residents of the region on the basis of qualitative case studies carried out in 2003 in the Chernobyl regions of Russia, Ukraine and Belarus. Our analysis indicates that informants tend to view their future as highly uncertain and unpredictable; they experience uncertainty about whether they are already contaminated, and they have to take hazardous decisions about where to go and what to eat. Fear, rumours and experts compete in supplying information to residents about the actual and potential consequences of the disaster, but there is little trust in, and only limited awareness of, the information that is provided. Most informants continue with their lives and do what they must or even what they like, even where the risks are known. They often describe their behaviour as being due to economic circumstances; where there is extreme poverty, even hazardous food sources are better than none. Unlike previous studies, we identify a pronounced tendency among informants not to separate the problems associated with the disaster from the hardships that have resulted from the break-up of the USSR, with both events creating a deep-seated sense of resignation and fatalism. Although most informants hold their governments to blame for lack of information, support and preventive measures, there is little or no collective action to have these put in place. This contrasts with previous research which has suggested that populations affected by disasters attribute crucial significance to that incident and, as a consequence, become increasingly politicized with regard to related policy agendas.

Phylogenetic analysis of porcine circovirus type 2 (PCV2) pre- and post-epizootic postweaning multisystemic wasting syndrome (PMWS)

The porcine circovirus type 2 (PCV2) genome encodes three major open reading frames (ORFs) encoding the replicase proteins (ORF1), the viral capsid protein (ORF2), and a protein with suggested apoptotic activity (ORF3). Previous phylogenetic analyses of complete genome sequences of PCV2 from GenBank have demonstrated 95-100% intra-group nucleotide sequence identity. However, although these isolates were readily grouped into clusters and clades, there was no correlation between the occurrence of specific PCV2 genotypes and the geographic origin or health status of the pig. In the present study, a unique dataset from a field study spanning the years pre and post the recognition of postweaning multisystemic wasting syndrome (PMWS) in Sweden was utilized. Using this dataset it was possible to discriminate three Swedish genogroups (SG1-3) of PCV2, of which SG1 was recovered from a pig on a healthy farm ten years before the first diagnosis of PMWS in Sweden. The SG1 PCV2/ORF2 gene sequence has been demonstrated to exhibit a high genetic stability over time and has subsequently only been demonstrated in samples from pigs on nondiseased farms. In contrast, SG2 was almost exclusively found on farms that had only recently broken down with PMWS whereas the SG3 genogroup predominated in pigs from PMWS-affected farms. These results further support the results obtained from earlier in vitro and in vivo experimental models and suggest the association of specific PCV2 genogroups with diseased and nondiseased pigs in the field.

Risk-informed decision-making in the presence of epistemic uncertainty

An important issue in risk analysis is the distinction between epistemic and aleatory uncertainties. In this paper, the use of distinct representation formats for aleatory and epistemic uncertainties is advocated, the latter being modelled by sets of possible values. Modern uncertainty theories based on convex sets of probabilities are known to be instrumental for hybrid representations where aleatory and epistemic components of uncertainty remain distinct. Simple uncertainty representation techniques based on fuzzy intervals and p-boxes are used in practice. This paper outlines a risk analysis methodology from elicitation of knowledge about parameters to decision. It proposes an elicitation methodology where the chosen representation format depends on the nature and the amount of available information. Uncertainty propagation methods then blend Monte Carlo simulation and interval analysis techniques. Nevertheless, results provided by these techniques, often in terms of probability intervals, may be too complex to interpret for a decision-maker and we, therefore, propose to compute a unique indicator of the likelihood of risk, called confidence index. It explicitly accounts for the decisionmaker’s attitude in the face of ambiguity. This step takes place at the end of the risk analysis process, when no further collection of evidence is possible that might reduce the ambiguity due to epistemic uncertainty. This last feature stands in contrast with the Bayesian methodology, where epistemic uncertainties on input parameters are modelled by single subjective probabilities at the beginning of the risk analysis process.

Incorporating uncertainty in predictive species distribution modelling

Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates.