bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach
Authors: Prieto-Calvo M.A. , Omer M.K. , Alvseike O. , López M. , Alvarez-Ordóñez A. , Prieto M. 
Published: January 2017

AbstractPhenotypic, chemotaxonomic and genotypic data from 12 strains ofEscherichia coli werecollected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems forE. coliand to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing ofE. colito species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification ofE. coli. The results showed that identification ofE. colistrains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.
A methodological framework to determine optimum durations for the construction of soil water characteristic curves using centrifugation
Authors: Vero Sara E. , Healy Mark G. , Henry Tiernan , Creamer Rachel E. , Ibrahim Tristan G. , Forrestal Patrick J. , Richards Karl G. , Fenton Owen 
Published: January 2017

AbstractDuring laboratory assessment of the soil water characteristic curve (SWCC), determining equilibrium at various pressures is challenging. This study establishes a methodological framework to identify appropriate experimental duration at each pressure step for the construction of SWCCs via centrifugation. Three common temporal approaches to equilibrium – 24-, 48- and 72-h – are examined, for a grassland and arable soil. The framework highlights the differences in equilibrium duration between the two soils. For both soils, the 24-h treatment significantly overestimated saturation. For the arable site, no significant difference was observed between the 48- and 72-h treatments. Hence, a 48-h treatment was sufficient to determine ‘effective equilibrium’. For the grassland site, the 48- and 72-h treatments differed significantly. This highlights that a more prolonged duration is necessary for some soils to conclusively determine that effective equilibrium has been reached. This framework can be applied to other soils to determine the optimum centrifuge durations for SWCC construction.
The costs of seasonality and expansion in Ireland’s milk production and processing
Authors: Heinschink K. , Shalloo L. , Wallace M. 
Published: January 2017

Abstract
Ireland’s milk production sector relies on grass-based spring-calving systems, which facilitates cost advantages in milk production but entails a high degree of supply seasonality. Among other implications, this supply seasonality involves extra costs in the processing sector including elevated plant capacities and varying levels of resource utilisation throughout the year. If both the national raw milk production increased substantially (e.g. post-milk quota) and a high degree of seasonality persisted, extra processing capacities would be required to cope with peak supplies. Alternatively, existing capacities could be used more efficiently by distributing the milk volume more evenly during the year. In this analysis, an optimisation model was applied to analyse the costs and economies arising to an average Irish milk-processing business due to changes to the monthly distribution of milk deliveries and/or the total annual milk pool. Of the situations examined, changing from a seasonal supply prior to expansion to a smoother pattern combined with an increased milk pool emerged as the most beneficial option to the processor because both the processor’s gross surplus and the marginal producer milk price increased. In practice, it may however be the case that the extra costs arising to the producer from smoothing the milk intake distribution exceed the processor’s benefit. The interlinkages between the stages of the dairy supply chain mean that nationally, the seasonality trade-offs are complex and equivocal. Moreover, the prospective financial implications of such strategies will be dependent on the evolving and uncertain nature of international dairy markets in the post-quota environment.
Developing farm-level sustainability indicators for Ireland using the Teagasc National Farm Survey
Authors: Ryan M. , Hennessy T. , Buckley C. , Dillon E.J. , Donnellan T. , Hanrahan K. , Moran B. 
Published: January 2017

Abstract
In the context of an expanding, export-dependent agri-food sector, indicators of sustainable development and intensification are necessary to measure, assess and verify the comparative advantage afforded by Ireland’s natural pastoral-based food production systems. Such indicators are also necessary to ensure that we produce more food with less adverse impacts on the Irish environment, climate and society. This article outlines the development of farm-level indicators that refect the multifaceted nature of sustainability, which is encompassed in economic, environmental and social indicators. The role of innovation in farm sustainability was also examined. A comparison of indicators across Irish farm systems showed that dairy farms, followed by tillage farms, tended to be the most economically and socially sustainable farm systems. In relation to greenhouse gas emissions in particular, the top-performing dairy farms, in an economic sense, also tended to be the best-performing farms from an environmental sustainability perspective. This trend was also evident in relation to the adoption of innovative practices on farm, which was found to be strongly correlated with economic performance.
Dairy product production and lactose demand in New Zealand and Ireland under different simulated milk product-processing portfolios
Authors: Sneddon N.W. , Lopez-Villalobos N. , Hickson R.E. , Davis S.R. , Geary U. , Garrick D.J. , Shalloo L. 
Published: January 2017

Abstract
Maximising dairy industry profitability involves maximising product returns for a specific set of costs or minimising costs for a certain level of output. A strategy currently utilised by the New Zealand dairy industry to optimise the value of exports is to incorporate imported lactose along with local milk to maximise the production of whole milk powder (WMP) while complying with the Codex Alimentarius (Codex) standards, in addition to increasing the exported product for every litre of milk. This study investigated the impact of different product portfolio strategies on lactose requirements for the Irish and New Zealand dairy industries for current and predicted 2020 milk output projections. A mass balance processing sector model that accounts for all inputs, outputs and losses involved in dairy processing was used to simulate the processing of milk into WMP, skim milk powder (SMP), cheese, butter and fluid milk of different proportions. All scenarios investigated projected an increase in production and revenue from 2012 to 2020. Higher cheese production reduced industry lactose demand through whey processing, while scenarios reliant on an increase in the proportion of WMP were associated with increased lactose deficits.
Response of two-row and six-row barley to fertiliser N under Irish conditions
Authors: Hackett R. 
Published: January 2017

Abstract
A range of cultivar types, including two-row and six-row types as well as line and hybrid types, are used for winter barley production in Ireland. There is little information available on the fertiliser nitrogen (N) requirements or the N use efficiency of these different types, particularly under Irish conditions. The objectives of the work presented here were to compare the response to fertiliser N of a two-row line cultivar, a six-row line cultivar and a six-row hybrid cultivar in terms of grain yield and aspects of N use efficiency. Experiments were carried out over three growing seasons, in the period 2012-2014, on a light-textured soil comparing the response of the three cultivars of winter barley to fertiliser N application rates ranging from 0 to 260 kg N/ha. There was no evidence that cultivar type, regardless of whether it was a two-row or six-row line cultivar or a six-row hybrid cultivar, influenced the response to fertiliser N of winter barley. There were some indications that six-row cultivars were less efficient at recovering soil N but used accumulated N more efficiently than the two-row cultivar. This work provided no evidence to support adjustment of fertiliser N inputs to winter barley based on cultivar type.
Detection of presumptive Bacillus cereus in the Irish dairy farm environment
Authors: O’Connell A. , Lawton E.M. , Leong D. , Cotter P. , Gleeson D. , Guinane C.M. 
Published: January 2017

AbstractThe objective of the study was to isolate potentialBacillus cereussensu lato (B.cereus s.l.)from a range of farm environments. Samples of tap water, milking equipment rinse water, milk sediment filter, grass, soil and bulk tank milk were collected from 63 farms. In addition, milk liners were swabbed at the start and the end of milking, and swabs were taken from cows’ teats prior to milking. The samples were plated on mannitol egg yolk polymyxin agar (MYP) and presumptiveB. cereus s.l. colonies were isolated and stored in nutrient broth with 20% glycerol and frozen at -80 °C. These isolates were then plated on chromogenic medium (BACARA) and colonies identified as presumptiveB. cereus s.l. on this medium were subjected to 16S ribosomal RNA (rRNA) sequencing. Of the 507 isolates presumed to beB. cereus s.l. on the basis of growth on MYP, only 177 showed growth typical ofB. cereus s.l. on BACARA agar. The use of 16S rRNA sequencing to identify isolates that grew on BACARA confirmed that the majority of isolates belonged toB. cereus s.l. A total of 81 of the 98 isolates sequenced were tentatively identified as presumptiveB. cereus s.l. Pulsed-field gel electrophoresis was carried out on milk and soil isolates from seven farms that were identified as having presumptiveB. cereus s.l. No pulsotype was shared by isolates from soil and milk on the same farm. PresumptiveB. cereus s.l. was widely distributed within the dairy farm environment.
A field-based comparison of ammonia emissions from six Irish soil types following urea fertiliser application
Authors: Burchill W. , Lanigan G.J. , Forrestal P.J. , Reville F. , Misselbrook T. , Richards K.G. 
Published: January 2017

AbstractAmmonia (NH3) emissions from a range of soil types have been found to differ under laboratory conditions. However, there is lack of studies comparing NH3emissions from different soil types under field conditions. The objective was to compare NH3emissions from six different soil types under similar environmental conditions in the field following urea fertiliser application. The study was conducted on a lysimeter unit and NH3emissions were measured, using wind tunnels, from six different soil types with varying soil characteristics following urea fertiliser application (80 kg N/ha). On average, 17.6% (% total N applied) was volatilised, and there was no significant difference in NH3emissions across all soil types. Soil variables, including pH, cation exchange capacity and volumetric moisture, were not able to account for the variation in emissions. Further field studies are required to improve the urea-NH3emission factor used for Ireland’s NH3inventory.
Electronic feeding behavioural data as indicators of health status in dairy calves
Authors: Johnston D. , Kenny D.A. , McGee M. , Waters S.M. , Kelly A.K. , Earley B. 
Published: January 2017

AbstractThe objectives of this study were (i) to characterise clinical health in dairy calves on an Irish research farm during the artificial calf-rearing period and (ii) to determine whether calves’ pre-weaning intakes and feeding behaviour, recorded by electronic calf feeders, changes in response to incidents of bovine respiratory disease (BRD). Holstein-Friesian (H-F) and Jersey (J) calves were fed by automatic milk replacer (MR) and concentrate feeders. Feeding behaviour, including MR consumption, drinking speed, number of rewarded and unrewarded visits to the feeder as well as concentrate consumption, was recorded by the feeders. A modified version of the Wisconsin calf health scoring criteria chart was used to score calves’ clinical measurements and identify incidences of BRD. Thus, 40% of calves were found to have at least one incident of BRD. Feeding behaviour was altered during incidents of BRD. The number of unrewarded visits to the feeder was reduced, by approximately four visits, for calves with BRD during the 3 d prior to the identification of BRD(P< 0.05) and tended to be reduced during the 7 d following the identification of BRD(P= 0.05), compared with healthy calves. Additionally, calves with BRD had a tendency for reduced net energy intake (approximately 8%) during the 3 d prior to the identification of BRD, compared with healthy calves. Therefore, calf feeding behavioural data, recorded by electronic feeders during the pre-weaning period, can indicate cases of BRD.
Effect of omitting teat preparation on bacterial levels in bulk tank milk
Authors: Gleeson David , Edwards Paul , O’Brien Bernadette 
Published: January 2017

Abstract
The objective of this study was to investigate the effect of omitting teat preparation prior to milking on the bacterial levels in milk directly after milking and after a period of milk storage. Eighty Holstein–Friesian dairy cows were assigned to two pre-milking teat preparation treatments: (i) washing of teats and drawing of foremilk, followed by drying with paper towels and (ii) no teat preparation. Individual cow measurements included individual quarter somatic cell count (SCC) and teat swabs for the presence of Bacillus cereus sensu lato. On seven monthly occasions, all milk produced over a 24 h period from each treatment group was segregated into a separate tank and sampled. Sub-samples of this milk were stored at 4 °C for 0, 24, 48 and 72 h, and the milk was analysed for total bacterial count (TBC), thermoduric bacterial count and the presence of B. cereus s. I. Individual quarter SCCs were numerically higher for unprepared teats (159,000 cells/mL) compared with those for prepared teats (133,000 cells/mL; P < 0.09). A similar trend was observed for bulk tank SCC, with the unprepared teat treatment tending to have a higher SCC (155,857 cells/mL) compared to the prepared teat treatment (102,286 cells/mL; P< 0.09). The TBC was not significantly higher from unprepared teats (3,152 cfu/ mL) compared with milk from prepared teats (1,678 cfu/mL) (P< 0.10). Milk TBC was significantly higher after storage for 72 h compared with that after 0, 24 and 48 h (P< 0.01). The results of this study indicate that under good hygienic conditions in an outdoor grazing situation, the omission of pre-milking teat preparation has a minimal effect on TBC and SCC.
A comparison of grassland vegetation from three agri-environment conservation measures
Authors: Ó hUallacháin D. , Finn J.A. , Keogh B. , Fritch R. , Sheridan H. 
Published: January 2017

AbstractSemi-natural grassland habitats have declined significantly throughout Europe. To halt the decline, grassland conservation measures have been included in most European agri-environment schemes. This is the first study to compare the botanical composition of grassland habitats managed under the Irish Agri-Environment Options Scheme (AEOS). Sixty fields on drystock pastoral farms in receipt of agri-environment payments for grassland conservation were surveyed, with 20 fields being enrolled in each of the following AEOS options: Traditional Hay Meadow (THM), Species-Rich Grassland (SRG) and Natura 2000 species-rich grassland (Natura). The vegetation quality of sites enrolled in the Natura measure was higher than the quality of those enrolled in the THM and SRG measures. Natura sites had the greatest species richness, with a mean >40 species per site, which included approximately 17 species indicative of high botanical quality. Traditional Hay Meadows sites had the lowest species richness (mean: 29 species per site) and were dominated by species associated with improved grassland. Some THM sites had good levels of botanical richness and were similar in composition to Natura sites, with some Natura sites having lower vegetation quality, more similar to that of THM sites. Species-Rich Grassland had botanical richness that was intermediate between THM and Natura sites. A thorough assessment of the effectiveness of these measures was confounded by a lack of quantitative objectives for the target community composition to be attained. We discuss limitations and potential opportunities regarding the design, targeting, implementation and cost-effectiveness of these agri-environment measures.
Behaviour of tail-docked lambs tested in isolation
Authors: Marchewka Joanna , Beltrán de Heredia Ina , Averós Xavier , Ruiz Roberto , Zanella Adroaldo J. , Calderón Díaz Julia Adriana , Estevez Inma 
Published: January 2017

AbstractThe aims of the current study were to detect behavioural indicators of pain of tail-docked sheep tested in isolation and to determine the relationship between behaviour and the pain levels to which they were exposed. Twenty-four female lambs, randomly assigned to four pens, had their tail docked with a rubber ring (TD; n = 6) without pain control procedures, TD with anaesthesia (TDA; n = 6) or TD with anaesthesia and analgesia (TDAA; n = 6). Additionally, six lambs handled but without tail docking or application of pain relief measures were used as the control (C). On the day prior (Day –1) to the TD and on days 1, 3 and 5 post-procedure, each lamb was individually removed from its group and underwent a 2.5 min open field test in a separate pen. Frequencies of behaviours such as rest, running, standing, walking and exploring were directly observed. Frequencies of exploratory climbs (ECs) and abrupt climbs (ACs) over the testing pen’s walls were video-recorded. Data were analysed using generalised linear mixed models with repeated measurements, including treatment and day as fixed effects and behaviour on Day –1 as a linear covariate. Control and TDAA lambs stood more frequently than TD lambs. TD lambs performed significantly more ACs compared to all other treatment groups. No other treatment effects were detected. A day effect was detected for all behaviours, while the EC frequency was highest for all tail-docked lambs on Day 5. Findings suggest that standing, ACs and ECs could be used as potential indicators of pain in isolated tail-docked lambs. However, differences in ECs between treatments only appeared 3 d after tail docking.
Local Entropy Production Rates in a Polymer Electrolyte Membrane Fuel Cell
Authors: Siemer Marc , Marquardt Tobias , Valadez Huerta Gerardo , Kabelac Stephan 
Published: January 2017

AbstractA modeling study on a polymer electrolyte membrane fuel cell by means of non-equilibrium thermodynamics is presented. The developed model considers a one-dimensional cell in steady-state operation. The temperature, concentration and electric potential profiles are calculated for every domain of the cell. While the gas diffusion and the catalyst layers are calculated with established classical modeling approaches, the transport processes in the membrane are calculated with the phenomenological equations as dictated by the non-equilibrium thermodynamics. This approach is especially instructive for the membrane as the coupled transport mechanisms are dominant. The needed phenomenological coefficients are approximated on the base of conventional transport coefficients. Knowing the fluxes and their intrinsic corresponding forces, the local entropy production rate is calculated. Accordingly, the different loss mechanisms can be detected and quantified, which is important for cell and stack optimization.
Pitfalls of Exergy Analysis
Authors: Vágner Petr , Pavelka Michal , Maršík František 
Published: January 2017

Abstract
The well-known Gouy–Stodola theorem states that a device produces maximum useful power when working reversibly, that is with no entropy production inside the device. This statement then leads to a method of thermodynamic optimization based on entropy production minimization. Exergy destruction (difference between exergy of fuel and exhausts) is also given by entropy production inside the device. Therefore, assessing efficiency of a device by exergy analysis is also based on the Gouy–Stodola theorem. However, assumptions that had led to the Gouy–Stodola theorem are not satisfied in several optimization scenarios, e.g. non-isothermal steady-state fuel cells, where both entropy production minimization and exergy analysis should be used with caution. We demonstrate, using non-equilibrium thermodynamics, a few cases where entropy production minimization and exergy analysis should not be applied.
Taboos and euphemisms in sex-related signs in Asian sign languages
Authors: Sze Felix Y. B. , Wei Monica Xiao , Wong Aaron Yiu Leung 
Published: January 2017

AbstractThis paper investigates sex-related euphemisms in four Asia sign languages, namely, Hong Kong Sign Language (HKSL), Jakarta Sign Language (JakSL) (Indonesia), Sri Lankan Sign Language (SLSL) and Japanese Sign Language (JSL). It aims at finding out if direct visual reference to sex-related body parts or concepts is taboo to Deaf signers and if this is the case, what strategies they adopt to form the corresponding euphemistic expressions. It will be argued that even though Deaf signers are used to the visual explicitness of the signing modality, the highly iconic nature of certain sex-related signs can still be offensive at times, thus giving rise to euphemistic expressions. While certain euphemistic strategies by the Deaf signers target at toning down the degree of visual iconicity originally associated with the taboo signs, most of the remaining strategies show striking resemblance to those used in spoken languages, suggesting the universality of these verbal politeness strategies across language modalities.