The universal functorial equivariant Lefschetz invariant

We introduce the universal functorial equivariant Lefschetz invariant for endomorphisms of finite proper G-CW-complexes, where G is a discrete group. We use K_0 of the category of "phi-endomorphisms of finitely generated free RPi(G,X)-modules". We derive results about fixed points of equivariant endomorphisms of cocompact proper smooth G-manifolds.Comment: 33 pages; shortened version of the author's PhD thesis, supervised by Wolfgang Lueck, Westfaelische Wilhelms-Universitaet Muenster, 200

An Epidemiological Investigation of the Re-Emergence of Pancreas Disease in Irish Farmed Atlantic Salmon (Salmo salar L.) in 2002

In the early 1990’s pancreas disease (PD) was shown to be the most significant cause of mortality in Irish farmed salmon (Wheatley et al., 1995, Menzies et al., 1996, Crockford et al., 1999). At that time the aetiology of PD was uncertain but in 1995 it was conclusively shown that PD was caused by a virus subsequently named salmon pancreas disease virus (SPDV), (Nelson et al., 1995, McLoughlin et al., 1996). It has since been further classified and named salmonid alphavirus (Weston et al., 1999, Weston et al., 2002). The clinical and histopathological features of naturally occurring pancreas disease in farmed Atlantic salmon in Ireland were described by Murphy et al., 1992 and McLoughlin et al., 2002. The original epidemiological studies of PD in Ireland indicated that mortality rates up to 48% have occurred in farmed Atlantic salmon in their first year in the sea on some individual fish farms (Menzies et al., 1996). PD was recorded in over 70% of marine sites monitored and the majority of PD outbreaks occurred during August to October (Crockford et al., 1999). A serological survey for the presence of SPDV antibody in 1996 revealed 53% of the sites (9/17) were positive and that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998). This pattern persisted until 2002 when there was a serious increase in both the incidence and severity of PD reported on farmed Atlantic salmon marine sites in Ireland. In order to identify factors associated with this re-emergence of PD in Irish farmed salmon, an in-depth epidemiological investigation was carried out on all marine sites. In trying to identify the cause of a disease from epidemiological studies the concept of time, place and individual is paramount, i.e. why did a particular disease occur in a particular animal or group of animals at a particular time in a particular place? Epidemiological study designs are chosen so that predictor variables are measured in affected and non-affected “units”. These “units” may be cells, animals, pens, farms or countries. The association between these predictor variables and disease is then examined. Where associations are demonstrated then risk factors for disease can be identified. A risk factor is a predictor variable associated with the disease. However the identification of a risk factor does not imply causation. The strength, consistency, temporality and dose response effect of the risk factor add weight to it being causal but only an intervention study where the risk factor is added or omitted can confirm this. Individual or univariate analysis of the relationship between a predictor variable and disease may result in an association being demonstrated. However it is dangerous to read too much into univariate analyses as factors which have been ignored, not measured or not seen as important may have a confounding effect. Multivariate analysis is used to try to provide estimates of association adjusted for the effect of confounding factors is a much more accurate and powerful epidemiological tool, but was of limited application in this snapshot survey of a single production cycle. This report aims to describe the occurrence and severity of PD in Irish farmed salmon in 2002-2003 and to identify risk factors associated with the re-emergence of severe PD. Finally, recommendations are made on how PD can be managed to reduce its serious impact on the health, welfare and productivity of Irish farmed salmon.Funder: Marine Institut

Fabrication and Assessment of 3D Printed Anatomical Models of the Lower Limb for Anatomical Teaching and Femoral Vessel Access Training in Medicine

For centuries, cadaveric dissection has been the touchstone of anatomy education. It offers a medical student intimate access to his or her first patient. In contrast to idealized artisan anatomical models, it presents the natural variation of anatomy in fine detail. However, a new teaching construct has appeared recently in which artificial cadavers are manufactured through three-dimensional (3D) printing of patient specific radiological data sets. In this article, a simple powder based printer is made more versatile to manufacture hard bones, silicone muscles and perfusable blood vessels. The approach involves blending modern approaches (3D printing) with more ancient ones (casting and lost-wax techniques). These anatomically accurate models can augment the approach to anatomy teaching from dissection to synthesis of 3D-printed parts held together with embedded rare earth magnets. Vascular simulation is possible through application of pumps and artificial blood. The resulting arteries and veins can be cannulated and imaged with Doppler ultrasound. In some respects, 3D-printed anatomy is superior to older teaching methods because the parts are cheap, scalable, they can cover the entire age span, they can be both dissected and reassembled and the data files can be printed anywhere in the world and mass produced. Anatomical diversity can be collated as a digital repository and reprinted rather than waiting for the rare variant to appear in the dissection room. It is predicted that 3D printing will revolutionize anatomy when poly-material printing is perfected in the early 21st century. (C) 2015 American Association of Anatomists

Fabrication and Assessment of 3D Printed Anatomical Models of the Lower Limb for Anatomical Teaching and Femoral Vessel Access Training in Medicine

For centuries, cadaveric dissection has been the touchstone of anatomy education. It offers a medical student intimate access to his or her first patient. In contrast to idealized artisan anatomical models, it presents the natural variation of anatomy in fine detail. However, a new teaching construct has appeared recently in which artificial cadavers are manufactured through three-dimensional (3D) printing of patient specific radiological data sets. In this article, a simple powder based printer is made more versatile to manufacture hard bones, silicone muscles and perfusable blood vessels. The approach involves blending modern approaches (3D printing) with more ancient ones (casting and lost-wax techniques). These anatomically accurate models can augment the approach to anatomy teaching from dissection to synthesis of 3D-printed parts held together with embedded rare earth magnets. Vascular simulation is possible through application of pumps and artificial blood. The resulting arteries and veins can be cannulated and imaged with Doppler ultrasound. In some respects, 3D-printed anatomy is superior to older teaching methods because the parts are cheap, scalable, they can cover the entire age span, they can be both dissected and reassembled and the data files can be printed anywhere in the world and mass produced. Anatomical diversity can be collated as a digital repository and reprinted rather than waiting for the rare variant to appear in the dissection room. It is predicted that 3D printing will revolutionize anatomy when poly-material printing is perfected in the early 21st century. (C) 2015 American Association of Anatomists

Aquaplan: health management for finfish aquaculture

Lead partner: Marine Institute, Oranmore, Co. Galway. Project Partners: Vet Aqua International, Oranmore, Co. Galway., Global Trust Certification Ltd., Dundalk, Co. Louth. Project duration: 01/10/2008 to 31/10/2011The AquaPlan project brought together key stakeholders from the finfish aquaculture industry and state agencies with the aim of drafting and implementing a national strategic plan for fish health in Ireland. Many countries already have well established comprehensive strategies for managing aquatic animal health which are deemed necessary for the sustainable development of the industry. A range of deliverables were produced by the project which are all essential components of the strategic plan for fish health management.Funder: Ireland's EU structural funds programme 2007-2013, co-funded by the Irish government and the European Union- European Regional Development Fund, Marine Institute. Grant-Aid agreement no. PBA/AF/08/003(01

Risk factors associated with increased mortality of farmed Pacific oysters in Ireland during 2011

Peer-reviewed. Released with a Creative Commons Attribution Non-Commercial No Derivatives LicenseThe Pacific oyster, Crassostrea gigas, plays a significant role in the aquaculture industry in Ireland. Episodes of increased mortality in C. gigas have been described in many countries, and in Ireland since 2008. The cause of mortality events in C. gigas spat and larvae is suspected to be multifactorial, with ostreid herpesvirus 1 (OsHV-1, in particular OsHV-1 μvar) considered a necessary, but not sufficient, cause. The objectives of the current study were to describe mortality events that occurred in C. gigas in Ireland during the summer of 2011 and to identify any associated environmental, husbandry and oyster endogenous factors. A prospective cohort study was conducted during 2010–2012, involving 80 study batches, located at 24 sites within 17 bays. All 17 bays had previously tested positive for OsHV-1 μvar. All study farmers were initially surveyed to gather relevant data on each study batch, which was then tracked from placement in the bay to first grading. The outcome of interest was cumulative batch-level mortality (%). Environmental data at high and low mortality sites were compared, and a risk factor analysis, using a multiple linear regression mixed effects model, was conducted. Cumulative batch mortality ranged from 2% to 100% (median = 16%, interquartile range: 10–34%). The final multivariable risk factor model indicated that batches imported from French hatcheries had significantly lower mortalities than non-French hatcheries; sites which tested negative for OsHV-1 μvar during the study had significantly lower mortalities than sites which tested positive and mortalities increased with temperature until a peak was reached. There were several differences between the seed stocks from French and non-French hatcheries, including prior OsHV-1 μvar exposure and ploidy. A range of risk factors relating to farm management were also considered, but were not found significant. The relative importance of prior OsHV-1 μvar infection and ploidy will become clearer with ongoing selection towards OsHV-1 μvar resistant oysters. Work is currently underway in Ireland to investigate these factors further, by tracking seed from various hatchery sources which were put to sea in 2012 under similar husbandry and environmental conditions

Detection of koi herpesvirus (KHV) in koi carp (Cyprinus carpio L.) imported into Ireland.

Peer-reviewedThis report described the first detections of koi herpesvirus (KHV) in the Republic of Ireland in imported koi carp. In both cases the KHV suspicions were confirmed by molecular diagnosis and the infected stocks culled.Funder: Marine Institut

The South Asian genome

Genetics of disease Microarrays Variant genotypes Population genetics Sequence alignment AllelesThe genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.Whole genome sequencing to discover genetic variants underlying type-2 diabetes, coronary heart disease and related phenotypes amongst Indian Asians. Imperial College Healthcare NHS Trust cBRC 2011-13 (JS Kooner [PI], JC Chambers)

Interface localisation-delocalisation transition in a symmetric polymer blend: a finite-size scaling Monte Carlo study

Using extensive Monte Carlo simulations we study the phase diagram of a symmetric binary (AB) polymer blend confined into a thin film as a function of the film thickness D. The monomer-wall interactions are short ranged and antisymmetric, i.e, the left wall attracts the A-component of the mixture with the same strength as the right wall the B-component, and give rise to a first order wetting transition in a semi-infinite geometry. The phase diagram and the crossover between different critical behaviors is explored. For large film thicknesses we find a first order interface localisation/delocalisation transition and the phase diagram comprises two critical points, which are the finite film width analogies of the prewetting critical point. Using finite size scaling techniques we locate these critical points and present evidence of 2D Ising critical behavior. When we reduce the film width the two critical points approach the symmetry axis $\phi=1/2$ of the phase diagram and for $D \approx 2 R_g$ we encounter a tricritical point. For even smaller film thickness the interface localisation/delocalisation transition is second order and we find a single critical point at $\phi=1/2$. Measuring the probability distribution of the interface position we determine the effective interaction between the wall and the interface. This effective interface potential depends on the lateral system size even away from the critical points. Its system size dependence stems from the large but finite correlation length of capillary waves. This finding gives direct evidence for a renormalization of the interface potential by capillary waves in the framework of a microscopic model.Comment: Phys.Rev.