The AFBI Repository

The Agri-Food and Biosciences Institute Repository collects, preserves, and makes freely available research outputs and related documents created by AFBI researchers, including peer-reviewed articles and conference papers. Where material has already been published it is made available subject to the open-access policies of the original publishers. About AFBI



Select a community to browse its collections.

Recent Submissions

Barriers and Enablers of Long-term Land Leasing: a Case Study of Northern Ireland
(Wiley, 2023-08-06) Adenuga, Adewale Henry; Jack, Claire; McCarry, Ronan; Caskie, Paul; Economics
Long-term land leasing offers a viable alternative to land ownership in relation to increasing efficiency of agricultural production, economies of scale, and delivering environmental improvements in terms of land management. However, with no significant tenanted sector in Northern Ireland, access to land via long-term land leasing is limited. This study analysed the barriers and enablers of long-term land leasing. To achieve our objective, we employed a mixed methods approach. The results show that the main barriers to long-term land leasing were environmental concern (around how the land will be managed), inheritance tax implications and the potential effect of long-term land leasing on future succession plans of the farm business. We also found that as much as 70 per cent of the farmers surveyed believe the inclusion of a ‘break clause’ and the introduction of income tax incentives will encourage the adoption of long-term land leasing, while 61 per cent of the farmers stated that the environmental management of the land will encourage long-term land leasing. The study concluded that any model designed to encourage long-term land leasing in Northern Ireland should include clauses which cover the environmental management of the land and break clauses. Income tax incentives for landowners could also be considered.
High-resolution assessment of riverbank erosion and stabilization techniques with associated water quality implications
(Taylor & Francis, 2023-05-26) Hayes, E.; Higgins, Suzanne; Mullan, D.; Geris, J.; Environmental Protection
Agriculture is a key contributor to poor water quality, but the sources of sediment and nutrient losses from agricultural catchments – including from riverbank erosion – are highly variable. Riverbank erosion is particularly difficult to quantify and control. Here, we developed a quick assessment approach to quantify riverbank erosion rates and associated sediment and nutrient loading rates into waterways using airborne LiDAR combined with field-collected data. We applied this approach and explored its relationships to water quality at four sites within the Blackwater catchment in Northern Ireland for two analysis periods. GIS LiDAR image differencing revealed that volume changes in riverbank elevation equated to average erosion rates which indicated spatial and temporal variability in erosion rates. Combining the erosion rates with in-situ riverbank bulk density and total extractable phosphorus content provided sediment and phosphorus loading rates. The relative differences between estimated erosion at the different sites corresponded well with in-stream suspended sediment variations, but patterns for total phosphorus concentrations were more complex. We conclude that the use of LiDAR combined with field data is an innovative means for riverbank erosion quantification. Furthermore, by using LiDAR-to-LiDAR analyses, the reductions in erosion, sediment, and phosphorus loading rates following riverbank stabilization techniques can be determined.
Machine learning in marine ecology: an overview of techniques and applications
(Oxford Univerity Press, 2023-08-03) Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Destro Barcellos, Diogo; Devos, Paul; Fernandes-Salvador, Jose A.; Fincham, Jennifer I.; Gomes, Alessandra; Handegard, Nils Olav; Howell, Kerry; Jamet, Cédric; Kartveit, Kyrre Heldal; Moustahfid, Hassan; Parcerisas, Clea; Politikos, Dimitris; Sauzède, Raphaëlle; Sokolova, Maria; Uusitalo, Laura; Van den Bulcke, Laure; van Helmond, Aloysius T. M.; Watson, Jordan T.; Welch, Heather; Beltran-Perez, Oscar; Chaffron, Samuel; Greenberg, David S.; Kühn, Bernhard; Kiko, Rainer; Lo, Madiop; Lopes, Rubens M.; Möller, Klas Ove; Michaels, William; Pala, Ahmet; Romagnan, Jean-Baptiste; Schuchert, Pia; Seydi, Vahid; Villasante, Sebastian; Malde, Ketil; Irisson, Jean-Olivier; Fisheries and Aquatic Ecosystems
Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.
Consumer assessment, in Ireland and the United Kingdom, of the impact of the method of suspension of carcasses from dairy-origin bulls and steers, on the sensory characteristics of the longissimus muscle
(Compuscript Ltd. on behalf of Teagasc, 2023-06-17) Moloney, A.P.; Chong, F.S.; Hagan, T.D.J.; Gordon, Alan W.; Methven, L.; O’Sullivan, M.G.; Farmer, Linda; Food Quality
The objective was to compare the assessment of beef produced in Ireland from a 19-month bull or a 24-month steer dairy beef production system by consumers in Ireland (Cork) and the United Kingdom (Belfast and Reading). Carcass sides were suspended by the Achilles tendon or by the pelvic bone and 21-d aged longissimus muscle assessed using Meat Standards Australia protocols. Carcass weight and classification were similar for bulls and steers. Consumers in Belfast and Cork rated aroma liking, tenderness, juiciness, overall liking and the composite meat quality score (MQ4) similarly, but lower (P < 0.05) than consumers in Reading. Consumers in Belfast and Cork rated flavour liking similarly as did consumers in Cork and Reading, but consumers in Reading rated flavour liking higher (P < 0.05) than consumers in Belfast. Muscle from steers had higher scores for aroma liking, flavour liking, overall liking and MQ4 scores than bulls (P < 0.05). On average, pelvic suspension increased (P < 0.05) the scores for aroma liking and flavour liking compared with conventional suspension but increased (P < 0.05) tenderness, juiciness, overall liking and MQ4 scores only in bulls. Consumers in Reading rated striploin from the traditional Achilles tendon-suspended steers similarly to striploin from pelvic-suspended bulls (MQ4 score of 71.8 and 68.2, respectively). Beef from the latter system could replace the traditional steer beef in this market, thereby benefiting the beef producer and the environment.
Natural Antimicrobials Block the Host NF-κB Pathway and Reduce Enterocytozoon hepatopenaei Infection Both In Vitro and In Vivo
(MDPI, 2023-07-20) Bundurus, Iulia Adelina; Balta, Igori; Butucel, Eugenia; Callaway, Todd; Popescu, Cosmin Alin; Iancu, Tiberiu; Pet, Ioan; Stef, Lavinia; Corcionivoschi, Nicolae; Animal Health and Welfare
The objective of this work was to investigate, for the first time, the antioxidant effect of a mixture of natural antimicrobials in an Enterocytozoon hepatopenaei (EHP) shrimp-gut model of infection and the biological mechanisms involved in their way of action. The study approach included investigations, firstly, in vitro, on shrimp-gut primary (SGP) epithelial cells and in vivo by using EHP-challenged shrimp. Our results show that exposure of EHP spores to 0.1%, 0.5%, 1%, and 2% AuraAqua (Aq) significantly reduced spore activity at all concentrations but was more pronounced after exposure to 0.5% Aq. The Aq was able to reduce EHP infection of SGP cells regardless of cells being pretreated or cocultured during infection with Aq. The survivability of SGP cells infected with EHP spores was significantly increased in both scenarios; however, a more noticeable effect was observed when the infected cells were pre-exposed to Aq. Our data show that infection of SGP cells by EHP activates the host NADPH oxidases and the release of H2O2 produced. When Aq was used during infection, a significant reduction in H2O2 was observed concomitant with a significant increase in the levels of CAT and SOD enzymes. Moreover, in the presence of 0.5% Aq, the overproduction of CAT and SOD was correlated with the inactivation of the NF-κB pathway, which, otherwise, as we show, is activated upon EHP infection of SGP cells. In a challenge test, Aq was able to significantly reduce mortality in EHP-infected shrimp and increase the levels of CAT and SOD in the gut tissue. Conclusively, these results show, for the first time, that a mixture of natural antimicrobials (Aq) can reduce the EHP-spore activity, improve the survival rates of primary gut-shrimp epithelial cells and reduce the oxidative damage caused by EHP infection. Moreover, we show that Aq was able to stop the H2O2 activation of the NF-κB pathway of Crustins, Penaeidins, and the lysozyme, and the CAT and SOD activity both in vitro and in a shrimp challenge test.