Higher-order compatible finite element schemes for the nonlinear rotating shallow water equations on the sphere

We describe a compatible finite element discretisation for the shallow water equations on the rotating sphere, concentrating on integrating consistent upwind stabilisation into the framework. Although the prognostic variables are velocity and layer depth, the discretisation has a diagnostic potential vorticity that satisfies a stable upwinded advection equation through a Taylor-Galerkin scheme; this provides a mechanism for dissipating enstrophy at the gridscale whilst retaining optimal order consistency. We also use upwind discontinuous Galerkin schemes for the transport of layer depth. These transport schemes are incorporated into a semi-implicit formulation that is facilitated by a hybridisation method for solving the resulting mixed Helmholtz equation. We illustrate our discretisation with some standard rotating sphere test problems.Comment: accepted versio

Fuel poverty, older people and cold weather: An all-island analysis

Executive Summary This report covers a number of different aspects of fuel poverty and older people. 1. An exploration of existing government survey data from Northern Ireland and the Republic of Ireland with a particular focus on older people and conducting additional targeted analyses where required. 2. An original survey in the Republic of Ireland exploring the lived experience of older people in cold weather. 3. A feasibility study of data logging thermometers placed in the homes of older tenants in local authority accommodation. 4. Analysis of excess winter mortality among older people including a consideration of differences between the two jurisdictions. Older people on the island of Ireland, as in many other countries, experience a ‘dual burden’ in terms of fuel poverty. They are more likely to experience fuel poverty and are also particularly vulnerable to health and social harm as a result of this experience. The numbers of older people vulnerable to ill-effects from cold homes will rise as numbers of people aged 80 and over, and those living with chronic illness or disability, increase. There were significant differences observed between expenditure-based, and subjective (EU-SILC) based fuel poverty indicators, for older people, and between Northern Ireland and Republic of Ireland data. This data required careful interpretation. The higher levels of fuel poverty recorded for older people on the island of Ireland appeared to be driven by all aspects of the fuel poverty model - poor housing condition, energy inefficient housing, rising fuel prices and low income. The majority of older people live in their own home and these homes tend to be older properties which are detached or semi-detached. Older people on the island are over-represented among houses which are in poor condition and which lack central heating in both jurisdictions. Lacking central heating was a more common experience for older people in the Republic of Ireland than in Northern Ireland. Data on energy efficiency measures were not comparable North/South but similar patterns were observed. Older people were less likely than the general population to have attic/loft or wall insulation or double glazing. Older people were also vulnerable from an income point of view. This would seem to be a particular issue in Northern Ireland where rates of income poverty are significantly increasing. In both jurisdictions older people were heavily reliant on social transfers to keep them out of poverty. Coupled with this, there is evidence that many older people are not claiming their full entitlements. Oil dependency was a particular issue in Northern Ireland. Very significant increases were observed in the price of heating oil, as well as electricity and gas in recent years. There was little available research evidence on the relationship between the older consumer and heating oil suppliers

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

peer-reviewedThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number:2012205

Temporal and spatial differences in microbial composition during the manufacture of a Continental-type cheese

peer-reviewedWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine salted Continental-type cheese in cheeses produced early and late in the production day. Differences in microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that late production day cheeses had a more diverse microbial population than their early day equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were found to initially have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas and Bifidobacterium, not routinely associated with a Continental-type cheese produced from pasteurised milk were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 201220

Deep spectroscopy of z~1 6C radio galaxies - II. Breaking the redshift-radio power degeneracy

The results of a spectroscopic analysis of 3CR and 6C radio galaxies at redshift z~1 are contrasted with the properties of lower redshift radio galaxies, chosen to be matched in radio luminosity to the 6C sources studied at z~1, thus enabling the P-z degeneracy to be broken. Partial rank correlations and principal component analysis have been used to determine which of z and P are the critical parameters underlying the observed variation of the ionization state andd kinematics of the emission line gas. [OII]/H-beta is shown to be a useful ionization mechanism diagnostic. Statistical analysis of the data shows that the ionization state of the emission line gas is strongly correlated with radio power, once the effects of other parameters are removed. No dependence of ionization state on z is observed, implying that the ionization state of the emission line gas is solely a function of the AGN properties rather than the hostt galaxy and/or environment. Statistical analysis of the kinematic properties of the emission line gas shows that these are strongly correlated independently withh both P and z. The correlation with redshift is the stronger of the two, suggesting that host galaxy composition or environment may play a role in producing the less extreme gas kinematics observed in the emission line regions of low redshift galaxies. For both the ionization and kinematic properties of thee galaxies, the independent correlations observed with radio size are strongest. Radio source age is a determining factor for the extended emission line regions.Comment: 10 pages, 5 figures, accepted for publication in MNRA

Continuous and discrete Clebsch variational principles

The Clebsch method provides a unifying approach for deriving variational principles for continuous and discrete dynamical systems where elements of a vector space are used to control dynamics on the cotangent bundle of a Lie group \emph{via} a velocity map. This paper proves a reduction theorem which states that the canonical variables on the Lie group can be eliminated, if and only if the velocity map is a Lie algebra action, thereby producing the Euler-Poincar\'e (EP) equation for the vector space variables. In this case, the map from the canonical variables on the Lie group to the vector space is the standard momentum map defined using the diamond operator. We apply the Clebsch method in examples of the rotating rigid body and the incompressible Euler equations. Along the way, we explain how singular solutions of the EP equation for the diffeomorphism group (EPDiff) arise as momentum maps in the Clebsch approach. In the case of finite dimensional Lie groups, the Clebsch variational principle is discretised to produce a variational integrator for the dynamical system. We obtain a discrete map from which the variables on the cotangent bundle of a Lie group may be eliminated to produce a discrete EP equation for elements of the vector space. We give an integrator for the rotating rigid body as an example. We also briefly discuss how to discretise infinite-dimensional Clebsch systems, so as to produce conservative numerical methods for fluid dynamics

High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

peer-reviewedBackground The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.This work was funded by the Department of Agriculture, Food and the Marine under the Food Institutional Research Measure through the ‘Cheeseboard 2015’ project. Daniel J. O’Sullivan is in receipt of a Teagasc Walsh Fellowship, Grant Number: 2012205