Assessing the sensitivity and specificity of fish community indicators to management action

We assessed ten trophodynamic indicators of ecosystem status for their sensitivity and specificity to fishing management using a size-resolved multispecies fish community model. The responses of indicators to fishing depended on effort and the size selectivity (sigmoid or Gaussian) of fishing mortality. The highest specificity against sigmoid (trawl-like) size selection was seen from inverse fishing pressure and the large fish indicator, but for Gaussian size selection, the large species indicator was most specific. Biomass, mean trophic level of the community and of the catch, and fishing in balance had the lowest specificity against both size selectivities. Length-based indicators weighted by biomass, rather than abundance, were more sensitive and specific to fishing pressure. Most indicators showed a greater response to sigmoid than Gaussian size selection. Indicators were generally more sensitive at low levels of effort because of nonlinear sensitivity in trophic cascades to fishing mortality. No single indicator emerged as superior in all respects, so given available data, multiple complementary indicators are recommended for community monitoring in the ecosystem approach to fisheries management.

Possible interactions between environmental factors in determining species optima

Questions: 1. Indicator values, such as those of Ellenberg, for different environmental factors are seen as independent. We tested for the presence of interactions between environmental factors ( soil moisture and reaction) to see if this assumption is simplistic. 2. How close are Ellenberg indicator values (IVs) related to the observed optima of species response curves in an area peripheral to those where they have been previously employed and 3. Can the inclusion of bryophytes add to the utility of IVs?

Location: South Uist, Outer Hebrides, Scotland, UK.

Methods: Two grids (ca. 2000 m x 2000 m) were sampled at 50-m intervals across the transition from machair to upland communities covering an orthogonal gradient of both soil pH ( reaction) and soil moisture content. Percentage cover data for vascular plants, bryophytes and lichens were recorded, along with pH and moisture content of the underlying sand/soil/peat. Reaction optima, derived from species response curves calculated using HOF models, were compared between wet and dry sites, and moisture optima between acidic and basic samples. Optima for the whole data set were compared to Ellenberg IVs to assess their performance in this area, with and without the inclusion of bryophytes.

Results: A number of species showed substantially different pH optima at high and low soil moisture contents (18% of those tested) and different soil moisture optima at high and low pH (49%). For a number of species the IVs were poor predictors of their actual distribution across the sampled area. Bryophytes were poor at explaining local variation in the environmental factors and also their inclusion with vascular plants negatively affected the strength of relationships.

Conclusions: A substantial number of species showed an interaction between soil moisture and reaction in determining their optima on the two respective gradients. It should be borne in mind that IVs such as Ellenberg's may not be independent of one another.

Are richness patterns of common and rare species equally well explained by environmental variables?

We investigated relationships between richness patterns of rare and common grassland species and environmental factors, focussing on comparing the degree to which the richness patterns of rare and common species are determined by simple environmental variables. Using data collected in the Machair grassland of the Outer Hebrides of Scotland, we fitted spatial regression models using a suite of grazing, soil physicochemical and microtopographic covariates, to nested sub-assemblages of vascular and non-vascular species ranked according to rarity. As expected, we found that common species drive richness patterns, but rare vascular species had significantly stronger affinity for high richness areas. After correcting for the prevalence of individual species distributions, we found differences between common and rare species in 1) the amount of variation explained: richness patterns of common species were better summarised by simple environmental variables, 2) the associations of environmental variables with richness showed systematic trends between common and rare species with coefficient sign reversal for several factors, and 3) richness associations with rare environments: richness patterns of rare vascular species significantly matched rare environments but those of non-vascular species did not. Richness patterns of rare species, at least in this system, may be intrinsically less predictable than those of common species.

Refractory cachexia and truth-telling about terminal prognosis; A qualitative study

The purpose of this paper is to examine the consequences that medical practitioners’ decisions about whether or not to be candid about terminal prognosis have for those suffering from refractory cachexia and their families. It presents the findings of a qualitative study which used focus groups and semi-structured interviews of a volunteer sample of doctors, nurses and dieticians in a cancer centre of a large teaching hospital in Northern Ireland. Respondents reported that some physicians tended to avoid discussing terminal prognosis in a direct manner with their patients. Nurses and dieticians tended to be reluctant to engage in conversations about weight loss with patients with cachexia. One of the reasons they reported for their lack of acknowledgement of weight loss concerned the close association between refractory cachexia and terminal prognosis. Because they viewed the telling of bad news as an exclusive prerogative of medical practitioners, they did not feel in a position to discuss cachexia because they were concerned that this had the potential to raise end-of-life issues that lay outside the boundaries of their professional role. This meant patients and their families were provided with little information about how to cope with the distressing consequences of cachexia.

Development and application of a multiple linear regression model to consider the impact of weekly waste container capacity on the yield from kerbside recycling programmes

The paper describes the development and application of a multiple linear regression model to identify how the key elements of waste and recycling infrastructure, namely container capacity and frequency of collection affect the yield from municipal kerbside recycling programmes. The overall aim of the research was to gain an understanding of the factors affecting the yield from municipal kerbside recycling programmes in Scotland. The study isolates the principal kerbside collection service offered by 32 councils across Scotland, eliminating those recycling programmes associated with flatted properties or multi occupancies. The results of a regression analysis model has identified three principal factors which explain 80% of the variability in the average yield of the principal dry recyclate services: weekly residual waste capacity, number of materials collected and the weekly recycling capacity. The use of the model has been evaluated and recommendations made on ongoing methodological development and the use of the results in informing the design of kerbside recycling programmes. The authors hope that the research can provide insights for the ongoing development of methods to optimise the design and operation of kerbside recycling programmes.

Long-range Transcriptome Sequencing Reveals Cancer Cell Growth Regulatory Chimeric mRNA

mRNA chimeras from chromosomal translocations often play a role as transforming oncogenes. However, cancer transcriptomes also contain mRNA chimeras that may play a role in tumor development, which arise as transcriptional or post-transcriptional events. To identify such chimeras, we developed a deterministic screening strategy for long-range sequence analysis. High-throughput, long-read sequencing was then performed on cDNA libraries from major tumor histotypes and corresponding normal tissues. These analyses led to the identification of 378 chimeras, with an unexpectedly high frequency of expression (˜2 x 10(-5) of all mRNA). Functional assays in breast and ovarian cancer cell lines showed that a large fraction of mRNA chimeras regulates cell replication. Strikingly, chimeras were shown to include both positive and negative regulators of cell growth, which functioned as such in a cell-type-specific manner. Replication-controlling chimeras were found to be expressed by most cancers from breast, ovary, colon, uterus, kidney, lung, and stomach, suggesting a widespread role in tumor development.

Phagocytic and serum killing of capsulate and non-capsulate Bacteroides fragilis

The relative susceptibilities of capsulate and non- capsulate variants of Bacteroides fragilis to serum and phagocytic killing were investigated. The capsule of B. fragilis did not confer resistance to serum killing. Phagocytic killing of non- capsulate B. fragilis occurred at bacterial concentrations of 1 X 10(6) and 1 X 10(7) cfu/ml. Capsulate B. fragilis organisms were also phagocytosed and killed at a concentration of 1 X 10(6) cfu/ml, but phagocytosis and killing were impaired at a concentration of 1 X 10(7) cfu/ml.

Immunochemical characterization of a polysaccharide antigen of Bacteroides fragilis with an IgM monoclonal antibody

An IgM mouse monoclonal antibody (McAb) Bf4 was produced to a surface polysaccharide of Bacteroides fragilis NCTC 9343. Immunoblotting showed that McAb Bf4 reacted strongly with a high molecular mass structure which was sensitive to oxidation with periodate but resisted protease treatment. An inhibition enzyme-linked immunosorbent assay (ELISA) indicated that McAb Bf4 did not cross react with the sixteen Bacteroides species and strains tested. Cells of B. fragilis NCTC 9343 recovered from the various interfaces of a Percoll discontinuous density gradient were tested in the inhibition ELISA. Bacteria from the 0-20%, 20-40% and 40-60% interfaces inhibited the ELISA; however, cells from the 60-80% interface did not. Electron microscopy with immunogold labelling showed that McAb Bf4 did not react with the extracellular fibrous network on bacteria recovered from the 0-20% interface, or the extracellular electron dense layer on cells from the 60-80% interface; however, it was associated with a surface structure on cells from the 20-40% interface. Growth in vivo did not enrich for bacteria with this structure.

Foraging trip time-activity budgets and reproductive success in the black-legged kittiwake

Seabirds are central place foragers during the breeding season and, as marine food resources are often patchily distributed, flexibility in foraging behaviour may be important in maintaining prey delivery rates to chicks. We developed a methodological approach using a combination of GPS data loggers and temperature-depth recorders that allowed us to describe the behaviour of surface-feeding seabirds. Specifically, we tested whether differences in foraging behaviour of black-legged kittiwakes Rissa tridactyla could be linked with reproductive success by comparing 2 consecutive years at 2 sites. At Rathlin Island (Northern Ireland) during 2010, foraging differed markedly from that during 2009 and from that at Lambay Island (Republic of Ireland) during both years. Birds exhibited foraging trips of greater duration, travelled a greater total distance, spent more time in transit and spent longer recuperating on the surface of the water. This notable shift was associated with a decline in breeding success, with greater loss of eggs to predation and lower prey delivery rates, resulting in the starvation of 15 % of chicks. We suggest that food resources were reduced or geographically less accessible during 2010, with suitable foraging areas located further from the colony. Birds did not invest greater amounts of time attempting to catch prey. Thus, our results indicate that kittiwakes at Rathlin modulated their foraging behaviour not by increasing foraging effort through feeding more intensively within prey patches but by extending their range to increase the probability of encountering more profitable prey patches. © Inter-Research 2012.

Non-adherence to therapy in children with cystic fibrosis

Hawthorne N., Hawwa A.F., Shields M.D., Reid A.J., McElnay J.C. (2011) Non-adherence to therapy in children with cystic fibrosis. Pediatric Pulmonology, 46: 408.