Multicenter Blinded Analysis of RT-PCR Detection Methods for Paramyxoviruses in Relation to Paget's Disease of Bone

Conflicting results have been reported on the detection of paramyxovirus transcripts in Paget's disease, and a possible explanation is differences in the sensitivity of RT-PCR methods for detecting virus. In a blinded study, we found no evidence to suggest that laboratories that failed to detect viral transcripts had less sensitive RT-PCR assays, and we did not detect measles or distemper transcripts in Paget's samples using the most sensitive assays evaluated.

Introduction: There is conflicting evidence on the possible role of persistent paramyxovirus infection in Paget's disease of bone (PDB). Some workers have detected measles virus (MV) or canine distemper virus (CDV) transcripts in cells and tissues from patients with PDB, but others have failed to confirm this finding. A possible explanation might be differences in the sensitivity of RT-PCR methods for detecting virus. Here we performed a blinded comparison of the sensitivity of different RT-PCR-based techniques for MV and CDV detection in different laboratories and used the most sensitive assays to screen for evidence of viral transcripts in bone and blood samples derived from patients with PDB.

Materials and Methods: Participating laboratories analyzed samples spiked with known amounts of MV and CDV transcripts and control samples that did not contain viral nucleic acids. All analyses were performed on a blinded basis.

Results: The limit of detection for CDV was 1000 viral transcripts in three laboratories (Aberdeen, Belfast, and Liverpool) and 10,000 transcripts in another laboratory (Manchester). The limit of detection for MV was 16 transcripts in one laboratory (NIBSC), 1000 transcripts in two laboratories (Aberdeen and Belfast), and 10,000 transcripts in two laboratories (Liverpool and Manchester). An assay previously used by a U.S.-based group to detect MV transcripts in PDB had a sensitivity of 1000 transcripts. One laboratory (Manchester) detected CDV transcripts in a negative control and in two samples that had been spiked with MV. None of the other laboratories had false-positive results for MV or CDV, and no evidence of viral transcripts was found on analysis of 12 PDB samples using the most sensitive RT-PCR assays for MV and CDV.

Conclusions: We found that RT-PCR assays used by different laboratories differed in their sensitivity to detect CDV and MV transcripts but found no evidence to suggest that laboratories that previously failed to detect viral transcripts had less sensitive RT-PCR assays than those that detected viral transcripts. False-positive results were observed with one laboratory, and we failed to detect paramyxovirus transcripts in PDB samples using the most sensitive assays evaluated. Our results show that failure of some laboratories to detect viral transcripts is unlikely to be caused by problems with assay sensitivity and highlight the fact that contamination can be an issue when searching for pathogens by sensitive RT-PCR-based techniques.

What is being taught in Religious Education classes in Northern Ireland and to what extent should states be concerned about regulation, quality and control of the subject?

This paper reports on a research project designed to discover what schools are teaching in Religious Education in Northern Ireland and what procedures are in place to maintain standards in the delivery of the subject. A search through literature shows that little research has been carried out to determine what is being taught in Religious Education in Northern Ireland. It also indicates that there are very weak systems of control to measure the effectiveness or quality of what is delivered. A survey of the websites of all Post-Primary schools in the region was used to provide some answers to the basic question of what is being taught in RE. Using content and discourse analysis of these alongside supporting documentary sources (textbooks and exam specifications), it is possible to get a clearer picture of how the Northern Ireland Core Syllabus for Religious Education and any additional curricular elements are delivered in schools. The findings show that a significant minority of schools do not publicly articulate what pupils do in religious education. In situations where the content of religious education is made clear, some definite trends are evident. Despite the existence of a statutory core syllabus, there is significant variation in what is taught in schools. The content is most divergent from the syllabus in relation to the teaching of World Religions at Key Stage 3 and at Key Stage 4 whole elements of the syllabus are neglected due to limited conformity between the syllabus and exam specifications. These results raise important questions about the systems of regulation and control of the subject in the region. In law the subject is exempt from formal inspection by the local inspection authority; instead, a form of inspection is allowed for by the Christian churches who design the syllabus, but it is a process that is either entirely neglected or entirely unreported in situations where it does occur. It is argued that these findings raise questions of more general concern for this and other regions in Europe where the teaching of religious education is largely unregulated. For example, to what extent should states take an interest in what is taught in religious education, how it is delivered, what values it promotes and how standards of teaching and learning in the subject are upheld?

The validity of classical trajectory and perturbative quantal methods for electron-impact ionization from excited states in H-like ions

To test the validity of classical trajectory and perturbative quantal methods for electron-impact ionization of H-like ions from excited states, we have performed advanced close-coupling calculations of ionization from excited states in H, Li 2+ and B 4+ using the R -matrix with pseudo states and the time-dependent close-coupling methods. Comparisons with our classical trajectory Monte Carlo (CTMC) and distorted-wave (DW) calculations show that the CTMC method is more accurate than the DW method for H, but does not improve with n and grows substantially worse with Z , while the DW method improves with Z and grows worse with n .

Site choices in recreational demand: a matter of utility maximization or regret minimization?

This paper compares the Random Regret Minimization and the Random Utility Maximization models for determining recreational choice. The Random Regret approach is based on the idea that, when choosing, individuals aim to minimize their regret – regret being defined as what one experiences when a non-chosen alternative in a choice set performs better than a chosen one in relation to one or more attributes. The Random Regret paradigm, recently developed in transport economics, presents a tractable, regret-based alternative to the dominant choice paradigm based on Random Utility. Using data from a travel cost study exploring factors that influence kayakers’ site-choice decisions in the Republic of Ireland, we estimate both the traditional Random Utility multinomial logit model (RU-MNL) and the Random Regret multinomial logit model (RR-MNL) to gain more insights into site choice decisions. We further explore whether choices are driven by a utility maximization or a regret minimization paradigm by running a binary logit model to examine the likelihood of the two decision choice paradigms using site visits and respondents characteristics as explanatory variables. In addition to being one of the first studies to apply the RR-MNL to an environmental good, this paper also represents the first application of the RR-MNL to compute the Logsum to test and strengthen conclusions on welfare impacts of potential alternative policy scenarios.

Mutagenesis of RpoE-like sigma factor genes in Bdellovibrio reveals differential control of groEL and two groES genes

BACKGROUND: Bdellovibrio bacteriovorus HD100 must regulate genes in response to a variety of environmental conditions as it enters, preys upon and leaves other bacteria, or grows axenically without prey. In addition to "housekeeping" sigma factors, its genome encodes several alternate sigma factors, including 2 Group IV-RpoE-like proteins, which may be involved in the complex regulation of its predatory lifestyle.

RESULTS: We find that one sigma factor gene, bd3314, cannot be deleted from Bdellovibrio in either predatory or prey-independent growth states, and is therefore possibly essential, likely being an alternate sigma 70. Deletion of one of two Group IV-like sigma factor genes, bd0881, affects flagellar gene regulation and results in less efficient predation, although not due to motility changes; deletion of the second, bd0743, showed that it normally represses chaperone gene expression and intriguingly we find an alternative groES gene is expressed at timepoints in the predatory cycle where intensive protein synthesis at Bdellovibrio septation, prior to prey lysis, will be occurring.

CONCLUSIONS: We have taken the first step in understanding how alternate sigma factors regulate different processes in the predatory lifecycle of Bdellovibrio and discovered that alternate chaperones regulated by one of them are expressed at different stages of the lifecycle.

The Application of Geophysics to a Number of Threats to Irish Soils

In its 2002 Communication "Towards a Thematic Strategy on Soil Protection" (COM 2002, 179), the Commission identified the main threats to which soils in the EU are confronted. More recently, the EU published a Thematic Strategy for Soil Protection (COM 2006, 231) as well as a proposal for a Soil Framework Directive (COM 2006, 232). The proposed directive, if implemented, will require states to identify a number of specific soil degradation processes that have occurred or are likely to occur in the near future. This project applies a number of recent geophysical developments, in addition to a range of traditional approaches, to a number of areas of Irish concern to Thematic Strategy for Soil Protection and the proposed Soil Framework Directive.

'Dare the boist'rous main': the role of the Belfast Newsletter in the process of emigration from Ulster to North America 1760-1800

Before the mass migrations from Ireland in the nineteenth century, earlier waves of migration in the eighteenth century saw significant numbers of people leave Ireland, predominantly from Ulster, to settle in North America. This article, using as its principal data source the Belfast News Letter ( BNL), its letters, advertisements and reports, focuses firstly on reconstructing the late eighteenth-century migration process and voyage, highlighting the barriers represented by the Atlantic Ocean. In addition to the challenges of the sea, there were problems with the ships, the ever-present danger of disease and also threats from other vessels, from privateers to press gangs. The voyage was recognized as a ‘universal dread’, and the risks taken to ‘dare the boist’rous main’ were perhaps not minimized in the pages of the BNL, whose editorial stance was antipathetic to the migration for the potential harm it caused to Ulster by removing so many of its industrious young. The second part of this article goes on to consider the newspaper’s and others’ vested interests in the emigration process, demonstrates how these were manifested in the press and sets the coverage of this very significant early emigration flow within the context of contemporary religious and colonial discourses at a period of very lively transatlantic interactions.