The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations

Cystic fibrosis (CF) is characterized by defective mucociliary clearance and chronic airway infection by a complex microbiota. Infection, persistent inflammation and periodic episodes of acute pulmonary exacerbation contribute to an irreversible decline in CF lung function. While the factors leading to acute exacerbations are poorly understood, antibiotic treatment can temporarily resolve pulmonary symptoms and partially restore lung function. Previous studies indicated that exacerbations may be associated with changes in microbial densities and the acquisition of new microbial species. Given the complexity of the CF microbiota, we applied massively parallel pyrosequencing to identify changes in airway microbial community structure in 23 adult CF patients during acute pulmonary exacerbation, after antibiotic treatment and during periods of stable disease. Over 350,000 sequences were generated, representing nearly 170 distinct microbial taxa. Approximately 60% of sequences obtained were from the recognized CF pathogens Pseudomonas and Burkholderia, which were detected in largely non-overlapping patient subsets. In contrast, other taxa including Prevotella, Streptococcus, Rothia and Veillonella were abundant in nearly all patient samples. Although antibiotic treatment was associated with a small decrease in species richness, there was minimal change in overall microbial community structure. Furthermore, microbial community composition was highly similar in patients during an exacerbation and when clinically stable, suggesting that exacerbations may represent intrapulmonary spread of infection rather than a change in microbial community composition. Mouthwash samples, obtained from a subset of patients, showed a nearly identical distribution of taxa as expectorated sputum, indicating that aspiration may contribute to colonization of the lower airways. Finally, we observed a strong correlation between low species richness and poor lung function. Taken together, these results indicate that the adult CF lung microbiome is largely stable through periods of exacerbation and antibiotic treatment and that short-term compositional changes in the airway microbiota do not account for CF pulmonary exacerbations.

Production and characterisation of monoclonal antibodies for the detection of AOZ, a tissue bound metabolite of furazolidone

3-amino-2-oxazolidinone (AOZ) is a tissue bound toxic metabolite derived from the nitrofuran antibiotic, furazolidone. AOZ is detected in the derivatised form of 3-{[(2-nitrophenyl) methylene]amino}-2-oxazolidinone (NP AOZ). 3-{[( 3- carboxyphenyl)-methylene]amino-2-oxazolidinone (CP AOZ) was used as the immunising hapten for the production of monoclonal antibodies against NP AOZ. Monoclonal antibodies were produced using hybridomas from the fusion of murine myeloma cells and spleen cells isolated from BALB/c mice immunised with CP AOZ-ethylenediamine-human serum albumin (CP AOZ-ed-HSA). The antibody production in ascitic fluids from clones 3B8/2B9 and 2D11/A4 was monitored during a 16 month period. Repeated cultures of these hybridomas, followed by injection into mice and cloning did not change the assay parameters. Clone 2D11/A4 exhibited long term stability in antibody production throughout the experiment whereas clone 3B8/2B9 demonstrated variability in particular antibody yields whilst retaining assay sensitivity. Reasons for this production variability in clones are discussed. In an optimised direct ELISA format, the antibodies exhibited a 50% binding inhibition in the range of 0.52-1.15 ng/ml with NP AOZ (0.22-0.50 ng/ml, respective AOZ equivalents) and showed high specificity towards this analyte. The sensitivity of monoclonal antibodies incorporated into the ELISA is compatible with the European Union MRLP and is currently in use for routine analysis.

How (In)Consistent is the Court of Justice in the Application of the Market Access Test?”

Invited panel speaker at a Jean Monnet Chair funded research workshop organised by the Europa Institute, School of Law, University of Edinburgh (9 December 2011), http://www.pol.ed.ac.uk/research_themes/index/jean_monnet_centre_of_excellence/principles_of_market_access_workshop

Social work education and political conflict: preparing students to address the needs of victims and survivors of the Troubles in Northern Ireland

This paper reports on the evaluation of a European PEACE III sponsored teaching and learning project that was designed to enable social work students to better understand the needs of victims and survivors of the conflict in Northern Ireland. The paper begins with an introduction to policy, practice and educational contexts before reviewing the literature on social work, conflict and trauma. It also summarises key, innovative pedagogical approaches used in the teaching, including the use of ground rules, teaching teams consisting of lecturer and service user dyads, learning exercises and case studies. The paper then explains the evaluation methodology. This involved two surveys which returned 144 student and 34 practice teacher questionnaires. The findings revealed that
students were generally committed to this form of teaching and engagement with victims and survivors of the conflict, although some students reported that their attitudes towards this subject had were not changed. Some students also discussed how the conflict had affected their lives and the lives of families and friends; it is argued that such biographical details are crucial in developing new pedagogical approaches in this area.
Practice teachers who supervised some of these students on placement reported general levels of satisfaction with preparedness to work with conflict related situations but were less convinced that organisations were so committed. The paper concludes with a discussion of the study limitations and a recommendation for more robust methods of teaching and evaluation in this area of social work education and practice.

Introduction

Introduction to edited collection, including historiographical review and summary of main contributions in ten-chapter volume.

Detonations in sub-chandrasekhar-mass C+O white dwarfs

Explosions of sub-Chandrasekhar-mass white dwarfs (WDs) are one alternative to the standard Chandrasekhar-mass model of Type Ia supernovae (SNe Ia). They are interesting since binary systems with sub-Chandrasekhar-mass primary WDs should be common and this scenario would suggest a simple physical parameter which determines the explosion brightness, namely the mass of the exploding WD. Here we perform one-dimensional hydrodynamical simulations, associated post-processing nucleosynthesis, and multi-wavelength radiation transport calculations for pure detonations of carbon-oxygen WDs. The light curves and spectra we obtain from these simulations are in good agreement with observed properties of SNe Ia. In particular, for WD masses from 0.97 to 1.15 Msun we obtain 56Ni masses between 0.3 and 0.8 Msun, sufficient to capture almost the complete range of SN Ia brightnesses. Our optical light curve rise times, peak colors, and decline timescales display trends which are generally consistent with observed characteristics although the range of B-band decline timescales displayed by our current set of models is somewhat too narrow. In agreement with observations, the maximum light spectra of the models show clear features associated with intermediate-mass elements and reproduce the sense of the observed correlation between explosion luminosity and the ratio of the Si II lines at ?6355 and ?5972. We therefore suggest that sub-Chandrasekhar-mass explosions are a viable model for SNe Ia for any binary evolution scenario leading to explosions in which the optical display is dominated by the material produced in a detonation of the primary WD. © 2010. The American Astronomical Society.

Job Strain as a Risk Factor for Leisure-Time Physical Inactivity: An Individual-Participant Meta-Analysis of Up to 170,000 Men and Women

Unfavorable work characteristics, such as low job control and too high or too low job demands, have been suggested to increase the likelihood of physical inactivity during leisure time, but this has not been verified in large-scale studies. The authors combined individual-level data from 14 European cohort studies (baseline years from 19851988 to 20062008) to examine the association between unfavorable work characteristics and leisure-time physical inactivity in a total of 170,162 employees (50 women; mean age, 43.5 years). Of these employees, 56,735 were reexamined after 29 years. In cross-sectional analyses, the odds for physical inactivity were 26 higher (odds ratio 1.26, 95 confidence interval: 1.15, 1.38) for employees with high-strain jobs (low control/high demands) and 21 higher (odds ratio 1.21, 95 confidence interval: 1.11, 1.31) for those with passive jobs (low control/low demands) compared with employees in low-strain jobs (high control/low demands). In prospective analyses restricted to physically active participants, the odds of becoming physically inactive during follow-up were 21 and 20 higher for those with high-strain (odds ratio 1.21, 95 confidence interval: 1.11, 1.32) and passive (odds ratio 1.20, 95 confidence interval: 1.11, 1.30) jobs at baseline. These data suggest that unfavorable work characteristics may have a spillover effect on leisure-time physical activity.

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data

The advent of next generation sequencing technologies (NGS) has expanded the area of genomic research, offering high coverage and increased sensitivity over older microarray platforms. Although the current cost of next generation sequencing is still exceeding that of microarray approaches, the rapid advances in NGS will likely make it the platform of choice for future research in differential gene expression. Connectivity mapping is a procedure for examining the connections among diseases, genes and drugs by differential gene expression initially based on microarray technology, with which a large collection of compound-induced reference gene expression profiles have been accumulated. In this work, we aim to test the feasibility of incorporating NGS RNA-Seq data into the current connectivity mapping framework by utilizing the microarray based reference profiles and the construction of a differentially expressed gene signature from a NGS dataset. This would allow for the establishment of connections between the NGS gene signature and those microarray reference profiles, alleviating the associated incurring cost of re-creating drug profiles with NGS technology. We examined the connectivity mapping approach on a publicly available NGS dataset with androgen stimulation of LNCaP cells in order to extract candidate compounds that could inhibit the proliferative phenotype of LNCaP cells and to elucidate their potential in a laboratory setting. In addition, we also analyzed an independent microarray dataset of similar experimental settings. We found a high level of concordance between the top compounds identified using the gene signatures from the two datasets. The nicotine derivative cotinine was returned as the top candidate among the overlapping compounds with potential to suppress this proliferative phenotype. Subsequent lab experiments validated this connectivity mapping hit, showing that cotinine inhibits cell proliferation in an androgen dependent manner. Thus the results in this study suggest a promising prospect of integrating NGS data with connectivity mapping. © 2013 McArt et al.

Community-acquired infections and their association with myeloid malignancies

Introduction: Antigenic stimulation is a proposed aetiologic mechanism for many haematological malignancies. Limited evidence suggests that community-acquired infections may increase the risk of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). However, associations with other myeloid malignancies including chronic myeloid leukaemia (CML) and myeloproliferative neoplasms (MPNs) are unknown.

Materials and methods: Using the Surveillance, Epidemiology and End Result (SEER)-Medicare database, fourteen community-acquired infections were compared between myeloid malignancy patients [AML (n=8489), CML (n=3626) diagnosed 1992-2005; MDS (n=3072) and MPNs (n=2001) diagnosed 2001-2005; and controls (200,000 for AML/CML and 97,681 for MDS/MPN]. Odds ratios (ORs) and 95% confidence intervals were adjusted for gender, age and year of selection excluding infections diagnosed in the 13-month period prior to selection to reduce reverse causality.

Results: Risk of AML and MDS respectively, were significantly associated with respiratory tract infections, bronchitis (ORs 1.20 [95% CI: 1.14-1.26], 1.25 [95% CI: 1.16-1.36]), influenza (ORs 1.16 [95% CI: 1.07-1.25], 1.29 [95% CI: 1.16-1.44]), pharyngitis (ORs 1.13 [95% CI: 1.06-1.21], 1.22 [95% CI: 1.11-1.35]), pneumonia (ORs 1.28 [95% CI: 1.21-1.36], 1.52 [95% CI: 1.40-1.66]), sinusitis (ORs 1.23 [95% CI: 1.16-1.30], 1.25 [95% CI: 1.15-1.36]) as was cystitis (ORs 1.13 [95% CI: 1.07-1.18], 1.26 [95% CI: 1.17-1.36]). Cellulitis (OR 1.51 [95% CI: 1.39-1.64]), herpes zoster (OR 1.31 [95% CI: 1.14-1.50]) and gastroenteritis (OR 1.38 [95% CI: 1.17-1.64]) were more common in MDS patients than controls. For CML, associations were limited to bronchitis (OR 1.21 [95% CI: 1.12-1.31]), pneumonia (OR 1.49 [95% CI: 1.37-1.62]), sinusitis (OR 1.19 [95% CI: 1.09-1.29]) and cellulitis (OR 1.43 [95% CI: 1.32-1.55]) following Bonferroni correction. Only cellulitis (OR 1.34 [95% CI: 1.21-1.49]) remained significant in MPN patients. Many infections remained elevated when more than 6 years of preceding claims data were excluded.

Discussion: Common community-acquired infections may be important in the malignant transformation of the myeloid lineage. Differences in the aetiology of classic MPNs and other myeloid malignancies require further exploration.

Risk of Several Cancers is Higher in Urban Areas after Adjusting for Socioeconomic Status. Results from a Two-Country Population-Based Study of 18 Common Cancers

Some studies suggest that there are urban-rural variations in cancer incidence but whether these simply reflect urban-rural socioeconomic variation is unclear. We investigated whether there were urban-rural variations in the incidence of 18 cancers, after adjusting for socioeconomic status. Cancers diagnosed between 1995 and 2007 were extracted from the population-based National Cancer Registry Ireland and Northern Ireland Cancer Registry and categorised by urban-rural status, based on population density of area of residence at diagnosis (rural 15 people per hectare). Relative risks (RR) were calculated by negative binomial regression, adjusting for age, country and three area-based markers of socioeconomic status. Risks were significantly higher in both sexes in urban than rural residents with head and neck (males RR urban vs. rural = 1.53, 95 % CI 1.42-1.64; females RR = 1.29, 95 % CI 1.15-1.45), esophageal (males 1.21, 1.11-1.31; females 1.21, 1.08-1.35), stomach (males 1.36, 1.27-1.46; females 1.19, 1.08-1.30), colorectal (males 1.14, 1.09-1.18; females 1.04, 1.00-1.09), lung (males 1.54, 1.47-1.61; females 1.74, 1.65-1.84), non-melanoma skin (males 1.13, 1.10-1.17; females 1.23, 1.19-1.27) and bladder (males 1.30, 1.21-1.39; females 1.31, 1.17-1.46) cancers. Risks of breast, cervical, kidney and brain cancer were significantly higher in females in urban areas. Prostate cancer risk was higher in rural areas (0.94, 0.90-0.97). Other cancers showed no significant urban-rural differences. After adjusting for socioeconomic variation, urban-rural differences were evident for 12 of 18 cancers. Variations in healthcare utilization and known risk factors likely explain some of the observed associations. Explanations for others are unclear and, in the interests of equity, warrant further investigation. © 2014 The New York Academy of Medicine.

Outcomes and process in reading tutoring

Background: Large-scale randomised controlled trials are relatively rare in education. The present study approximates to, but is not exactly, a randomised controlled trial. It was an attempt to scale up previous small peer tutoring projects, while investing only modestly in continuing professional development for teachers.Purpose: A two-year study of peer tutoring in reading was undertaken in one local education authority in Scotland. The relative effectiveness of cross-age versus same-age tutoring, light versus intensive intervention, and reading versus reading and mathematics tutoring were investigated.Programme description (if relevant): The intervention was Paired Reading, a freely available cross-ability tutoring method applied to books of the pupils' choice but above the tutee's independent readability level. It involves Reading Together and Reading Alone, and switching from one to the other according to need.Sample: Eighty-seven primary schools of overall average socio-economic status, ability and gender in one council in Scotland. There were few ethnic minority students. Proportions of students with special needs were low. Children were eight and 10 years old as the intervention started. Macro-evaluation n = 3520. Micro-evaluation Year 1 15 schools n = 592, Year 2 a different 15 schools n = 591, compared with a comparison group of five schools n = 240.Design and methods: Almost all the primary schools in the local authority participated and were randomly allocated to condition. A macro-evaluation tested and retested over a two-year period using Performance Indicators in Primary Schools. A micro-evaluation tested and retested within each year using norm-referenced tests of reading comprehension. Macro-evaluation was with multi-level modelling, micro-evaluation with descriptive statistics and effect sizes, analysis of variance (ANOVA) and multivariate analysis of variance (MANOVA).Results: Macro-evaluation yielded significant pre-post gains in reading attainment for cross-age tutoring over both years. No other differences were significant. Micro-evaluation yielded pre-post changes in Year 1 (selected) and Year 2 (random) greater than controls, with no difference between same-age and cross-age tutoring. Light and intensive tutoring were equally effective. Tutoring reading and mathematics together was more effective than only tutoring reading. Lower socio-economic and lower reading ability students did better. Girls did better than boys. Regarding observed implementation quality, some factors were high and others low. Few implementation variables correlated with attainment gain.Conclusions: Paired Reading tutoring does lead to better reading attainment compared with students not participating. This is true in the long term (macro-evaluation) for cross-age tutoring, and in the short term (micro-evaluation) for both cross-age and same-age tutoring. Tutors and tutees benefited. Intensity had no effect but dual tutoring did have an effect. Low-socio-economic status, low-ability and female students did better. The results of the different forms of evaluation were indeed different. There are implications for practice and for future research. © 2012 Copyright Taylor and Francis Group, LLC.

Common community-acquired infections and subsequent risk of multiple myeloma: a population-based study

The role of bacteria and viruses as aetiological agents in the pathogenesis of cancer has been well established for several sites, including a number of haematological malignancies. Less clear is the impact of such exposures on the subsequent development of multiple myeloma (MM). Using the population-based U.S. Surveillance Epidemiology and End Results-Medicare dataset, 15,318 elderly MM and 200,000 controls were identified to investigate the impact of 14 common community-acquired infections and risk of MM. Odds ratios (ORs) and associated 95% confidence intervals (CIs) were adjusted for sex, age and calendar year of selection. The 13-month period prior to diagnosis/selection was excluded. Risk of MM was increased by 5-39% following Medicare claims for eight of the investigated infections. Positive associations were observed for several infections including bronchitis (adjusted OR 1.14, 95% CI 1.09-1.18), sinusitis (OR 1.15, 95% CI 1.10-1.20) pneumonia (OR 1.27, 95% CI 1.21-1.33), herpes zoster (OR 1.39, 95% CI 1.29-1.49) and cystitis (OR 1.09, 95% CI 1.05-1.14). Each of these infections remained significantly elevated following the exclusion of more than 6 years of claims data. Exposure to infectious antigens may therefore play a role in the development of MM. Alternatively, the observed associations may be a manifestation of an underlying immune disturbance present several years prior to MM diagnosis and thereby part of the natural history of disease progression.

2-D R-matrix Propagator: Application and Future Developments

Ongoing developments of the 2-D R-matrix propagator are discussed. These include application to electron and photon collisions with H-like ions; computational innovations; and important theoretical developments to enable the accurate treatment of electron and photon collisions with multi-electron atoms at intermediate energies.