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More than a whistle: Automated detection of marine sound sources with a convolutional neural network
Get PDFPublication history: Accepted - 14 September 2022; Published online - 04 October 2022The effective analysis of Passive Acoustic Monitoring (PAM) data has the potential to determine spatial and temporal variations in ecosystem health and species presence if automated detection and classification algorithms are capable of discrimination between marine species and the presence of anthropogenic and environmental noise. Extracting more than a single sound source or call type will enrich our understanding of the interaction between biological, anthropogenic and geophonic soundscape components in the marine environment. Advances in extracting ecologically valuable cues from the marine environment, embedded within the soundscape, are limited by the time required for manual analyses and the accuracy of existing algorithms when applied to large PAM datasets. In this work, a deep learning model is trained for multi-class marine sound source detection using cloud computing to explore its utility for extracting sound sources for use in marine mammal conservation and ecosystem monitoring. A training set is developed comprising existing datasets amalgamated across geographic, temporal and spatial scales, collected across a range of acoustic platforms. Transfer learning is used to fine-tune an open-source state-of-the-art ‘small-scale’ convolutional neural network (CNN) to detect odontocete tonal and broadband call types and vessel noise (from 0 to 48 kHz). The developed CNN architecture uses a custom image input to exploit the differences in temporal and frequency characteristics between each sound source. Each sound source is identified with high accuracy across various test conditions, including variable signal-to-noise-ratio. We evaluate the effect of ambient noise on detector performance, outlining the importance of understanding the variability of the regional soundscape for which it will be deployed. Our work provides a computationally low-cost, efficient framework for mining big marine acoustic data, for information on temporal scales relevant to the management of marine protected areas and the conservation of vulnerable species.This work was supported by the Natural Environmental Research Council [grant number NE/S007210/1]. The COMPASS project has been supported by the EU’s INTERREG VA Programme, managed by the Special EU Programmes Body. The views and opinions expressed in this document do not necessarily reflect those of the European Commission or the Special EU Programmes Body (SEUPB)
The likely suspect’s framework: the need for a life cycle approach for managing Atlantic salmon (Salmo salar) stocks across multiple scales
Get PDFPublication history: Accepted - 10 May 2022: Published online - 8 June 2022The ongoing declines in Atlantic salmon populations across its range underscore the need for co-ordinated scientific-based knowledge to support
management and decisions for their conservation. Current salmon management actions remain largely focused on addressing bottlenecks to
production in the freshwater phase of the life-cycle, whereas the continued declines observed in the recent decades are thought to be driven
primarily by constraints on the marine phase. The challenges brought by global warming and other emerging stressors require immediate actions,
requiring us to re-think the methods behind stock assessment and forge stronger linkages between data, models and policies to promote more
effective management actions. We outline a scientific framework that takes a wider ecosystem view, designed to evaluate holistically a suite
of indicators and potential drivers of salmon mortality at key phases of the life cycle. The aims of the proposed “Likely Suspects Framework”
are to enhance cross-fertilisation of ideas between assessment processes at the stock-complex scale and stock-specific focused management
activities, and to develop new decision support tools to improve management efficiencies and scenario testing. Adopting such an approach
provides a new way to catalyse the acquisition and deployment of both existing and new data and models that are urgently needed for assisting
the conservation and future stewardship of salmon stocks on both sides of the Atlantic.This work was supported largely by funding from the UK Missing Salmon Allianc
The accumulation of microplastic pollution in a commercially important fishing ground.
Get PDFPublication history: Accepted - 3 March 2022; Published online - 10 March 2022The Irish Sea is an important area for Norway Lobster Nephrops norvegicus fisheries, which are the most valuable fishing resource in the UK. Norway lobster are known to ingest microplastic pollution present in the sediment and have displayed reduced body mass when exposed to microplastic pollution. Here, we identified microplastic pollution in the Irish Sea fishing grounds through analysis of 24 sediment samples from four sites of differing proximity to the Western Irish Sea Gyre in both 2016 and 2019. We used µFTIR spectroscopy to identify seven polymer types, and a total of 77 microplastics consisting of fibres and fragments. The mean microplastics per gram of sediment ranged from 0.13 to 0.49 and 0 to 1.17 MP/g in 2016 and 2019, respectively. There were no differences in the microplastic counts across years, and there was no correlation of microplastic counts with proximity to the Western Irish Sea Gyre. Considering the consistently high microplastic abundance found in the Irish Sea, and the propensity of N. norvegicus to ingest and be negatively impacted by them, we suggest microplastic pollution levels in the Irish Sea may have adverse impacts on N. norvegicus and negative implications for fishery sustainability in the future.EMC is supported by the Department for Agriculture, Environment and Rural Affairs Northern Ireland. NHJ is supported by an Envision Doctoral Training Programme Scholarship funded by the UK National Environment Research Council (NERC). EMC gratefully thanks Dave Williams and Hazel Clark for their technical assistance, Prof Jochen H. E. Koop for facilitating the µFTIR analysis at the Federal Institute of Hydrology, BfG, Koblenz, Germany, and Dr Jason Kirby for facilitating the microplastic analysis at Liverpool John Moores University
How Cover Crop Sowing Date Impacts upon Their Growth, Nutrient Assimilation and the Yield of the Subsequent Commercial Crop
Get PDFPublication history: Accetpted - 24 January 2022; Published online - 1 February 2022Cover crops are typically sown post-harvest of commercial crops, prior to winter, which means that as sowing date is delayed, so will biomass production potential. The wide range of benefits associated with cover crops relies on them to produce sufficient biomass. Therefore, it must be identified how late certain species of cover crops can be sown. In the climatic conditions of Northern Ireland, not only has no research been conducted on how cover crops perform at various sowing dates but also their effect on the subsequent commercial crop yield has not been investigated. Addressing these issue will in turn help provide recommendations to maximise and encourage later sowing of cover crops. Consequently, five species of cover crops were chosen, from a range of families, then sown on 14 August, 7 September and 27 September. This is to mimic when land becomes fallow post-harvest of typical crops/rotations to this region. It was found that tillage radish (Raphanus sativus L.), when sown on the earliest date, could accumulate a maximum of 261 kg/ha of nitrogen (N), whereas, when sown on the last date, phacelia (Phacelia tanacetifolia L.) significantly outperformed all other species and assimilated 70 kg/ha of N. The cover crops were then incorporated into the soil and over-sown with spring barley (Hordeum vulgare L.). However, the spring barley yield was unaffected by any treatments. This trial shows that the non-leguminous species chosen are highly effective in assimilating nutrients when sown mid-August until early-SeptemberThis research was funded by DAERA grant number (17/1/01
Effect of reduced dietary protein level on finishing pigs’ harmful social behaviour before and after an abrupt dietary change.
No full textPublication history: Accepted - 3 October 2022; Published online - 6 October 2022Tail biting in pigs is a harmful behavioural disorder that negatively affects their welfare. Nutrition has played a crucial role in improving farm efficiency; however, an imbalance in key nutrients is an accepted risk factor for tail biting. The exact contributing factors and the level of risk associated with inadequate nutrition remain unclear. We aimed to assess the effect of dietary protein level on harmful social behaviours in finishing pigs before and after an abrupt dietary change. A total of 80 pigs (Duroc x (Landrace x Large White)) were assigned to this trial over two batches. Pigs were housed in mixed sex groups of 10 and assigned to one of two treatments at 12 weeks of age. These consisted of a control treatment (CON) containing 15.5% Crude Protein (CP) and a low CP treatment (LowCP) containing 13.5% CP. The abrupt dietary change occurred at 16 weeks of age (71.45 kg) in batch 1 and at 15 weeks of age (67.04 kg) in batch 2. This change in diet led to a 1.2% drop in CP in the CON treatment and a 1.4% drop in CP in the LowCP treatment. Behavioural observations were performed before and after the diet change and largely focused on the pigs' social behaviour. Using a "hurdle" model analysis, we investigated whether diet, diet change or sex influenced: 1) the probability that a behaviour was not performed, and 2) the frequency and/or duration when the behaviour was performed. The LowCP treatment led to an increased duration of limb-directed behaviour (P = 0.03) when performed at all, and also an increased duration of ‘tail-in-mouth’ behaviour (P = 0.02) in males but not females. However, LowCP did not affect the level of ear-directed behaviours in this way (P > 0.05). An increase in standing frequency occurred after the abrupt diet change (P = 0.04). Our study indicates that a small reduction in dietary protein and sex affect behaviour in the finishing phase, with some impacts on important harmful social behaviours. Furthermore, an effect of abrupt diet change on behaviour is suggested, which will require further confirmation
Consequences of timing of organic enrichment provision on pig performance, health and stress resilience after weaning and regrouping
Get PDFPublication history: Accepted - 20 August 2022; Published online - 29 September 2022Most pigs in slatted systems are provided with enrichment meeting only minimum legal requirements. We aimed to explore the effects of a novel enrichment treatment consisting of daily provided fodder beet and jute bags for pigs in slatted systems, and investigate the timing of enrichment provision on performance, health and stress resilience. We used 280 weaners allocated into standard (S, meeting only legal requirements consisting of a plastic toy and softwood) or enriched (E) treatment (n = 14 groups/treatment). At regrouping during the grower to finisher transition, pigs were either kept in the same treatment (EE, SS) or switched from enriched to standard (ES) and vice versa (SE); each treatment was replicated on five groups. Pigs were weighted at the start and end of weaner, and finisher stage, and feed intake was recorded. Occurrence of scouring, respiratory problems, locomotor disorders, tail, ear, and body lesions were recorded twice a week. Ten males per treatment were sampled for saliva on days 1, 2 and 4, either postweaning or after the housing switch. Saliva samples were analysed for cortisol, alpha-amylase, haptoglobin (Hp), and adenosine deaminase. Additionally, these pigs were sampled for hair at the start and end of weaner, and end of finisher stage to analyse for hair cortisol and cortisone. We found that E weaners consumed less feed (P = 0.04), had better FCR (feed conversion ratio, P = 0.03) and less ear lesions for two weeks postweaning (P = 0.04), and tended to have lower occurrence of scouring (P = 0.07) and higher salivary cortisol concentrations (P = 0.09) than S weaners. Effects of enrichment treatment during weaner stage on performance were carried through to finisher stage, with EE and ES pigs having better FCR (P = 0.0009) and higher BW (P = 0.0001) compared to SS and SE pigs. E treatment during finisher stage decreased feed intake (P = 0.04) and tended to decrease Hp levels (P = 0.07). There was a significant interaction between enrichment treatments during weaner and finisher stages on finisher body lesions: EE finishers had less lesions than SS, ES, and SE finishers (P = 0.04). There were no other significant differences caused either by enrichment treatment during weaner/finisher stage or their interaction. We conclude that the novel enrichment applied at weaner stage had positive effects on ear lesions and performance, which were carried through to finisher stage. Body lesions were affected by its application during both stages, with finishers receiving the enrichment treatment throughout (EE) having reduced body lesions than the rest of the finishers.This research was part of the EU-China HealthyLivestock project. The authors wish to acknowledge that HealthyLivestock is funded by the European Union H2020 research and innovation programme under grant agreement number 773436. The European Commission’s support for the production of this publication does not constitute an endorsement of the contents, which reflect the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein
Grassland Reseeding: Impact on Soil Surface Nutrient Accumulation and Using LiDAR-Based Image Differencing to Infer Implications for Water Quality
Get PDFPublication history: Accepted - 2 November 2022; Published - 4 November 2022.Long-term phosphorus (P) accumulation in agricultural soils presents a challenge for water
quality improvement. P is commonly elevated in soils managed for intensive livestock production
due to repeated overapplication of slurry and fertilisers. High legacy nutrient accumulations result
in poor water quality via transport pathways such as surface runoff, subsurface drainage, and
soil erosion. To achieve environmental water quality targets, improved management strategies
are required for targeting and reducing excess agricultural P sources. Reseeding of old swards is
known to improve grassland productivity and enhance overall soil health. However, soil disturbance
associated with reseeding could have positive and negative impacts on other soil functions that
affect the nutrient balance (including improved microbial activity, but also increasing the potential
for sediment and nutrient losses). This study investigates the impact of reseeding and inversion
tillage in addressing soil surface nutrient surpluses and identifies potential trade-offs between
production, environment (through soil erosion and associated sediment and nutrient losses), and
soil health. At a study site in the Blackwater catchment in Northern Ireland, we collected highresolution
(35 m) gridded soil samples pre- and post-reseeding for nutrient analyses and combined
this with GIS-based interpolation. We found that decreases in sub-field scale surface nutrient content
(0–7.5 cm depth) occurred following tillage and reseeding, but that this was spatially variable. In
addition, the magnitude of changes in nutrient content was variable between P and other sampled
nutrients. LiDAR-based image differencing indicated variability in the magnitude of soil erosion
and sediment loss also at sub-field scale. Information on the identified deposition and erosion zones
(from LiDAR analysis) was combined with mass wasting data to determine accumulation rates and
losses of nutrients in-field and confirmed some of the identified patterns in soil surface nutrient
content changes post-reseeding. We conclude that while inversion tillage and reseeding are essential
agricultural practices, environmental trade-offs exist through potential nutrient and sediment losses.
LiDAR-based image differencing was found to be a useful tool in helping to quantify these risks.
Quantifying sediment and nutrient losses as a result of inversion tillage and reseeding induced soil
erosion aids in understanding potential trends in water quality statuses.This research was funded by the NERC QUADRAT DTP, grant number 2280708
Proportion of Concentrate in the Diet of Early Lactation Dairy Cows has Contrasting effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility according to Parity
Get PDFPublication history: Accepted - 16 December 2022; Published online - 20 December 2022The functionality of circulating leukocytes in dairy cows is suppressed after calving, with negative energy balance as a risk factor. Leukocyte transcriptomic profiles were compared separately in 44 multiparous (MP) and 18 primiparous (PP) Holstein–Friesian cows receiving diets differing in concentrate proportion to test whether immune dysfunction could be mitigated by appropriate nutrition. After calving, cows were offered either (1) low concentrate (LC); (2) medium concentrate (MC) or (3) high concentrate (HC) diets with proportions of concentrate to grass silage of 30%:70%, 50%:50% and 70%:30%, respectively. Cow phenotype data collected included circulating metabolites, milk yield and health and fertility records. RNA sequencing of circulating leukocytes at 14 days in milk was performed. The HC diet improved energy balance in both age groups. There were more differentially expressed genes in PP than MP cows (460 vs. 173, HC vs. LC comparison) with few overlaps. The MP cows on the LC diet showed upregulation of the complement and coagulation cascade and innate immune defence mechanisms against pathogens and had a trend of more cases of mastitis and poorer fertility. In contrast, the PP cows on the HC diet showed greater immune responses based on both gene expression and phenotypic data and longer interval of calving to conception. The leukocytes of MP and PP cows therefore responded differentially to the diets between age, nutrient supply and immunity affecting their health and subsequent fertility.This project received funding from the European Union’s Seventh Framework Programme (EU FP7, Brussels, Belgium) for research, technological development, and demonstration under grant agreement no. 613689 (GplusE). The views expressed in this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission
Strategies for Hypothermia Compensation in Altricial and Precocial Newborn Mammals and Their Monitoring by Infrared Thermography
Get PDFPublication history: Accepted - 18 May 2022; Published - 23 May 2022.Thermoregulation in newborn mammals is an essential species-specific mechanism of the
nervous system that contributes to their survival during the first hours and days of their life. When
exposed to cold weather, which is a risk factor associated with mortality in neonates, pathways
such as the hypothalamic–pituitary–adrenal axis (HPA) are activated to achieve temperature control,
increasing the circulating levels of catecholamine and cortisol. Consequently, alterations in blood
circulation and mechanisms to produce or to retain heat (e.g., vasoconstriction, piloerection, shivering,
brown adipocyte tissue activation, and huddling) begin to prevent hypothermia. This study aimed
to discuss the mechanisms of thermoregulation in newborn domestic mammals, highlighting the
differences between altricial and precocial species. The processes that employ brown adipocyte
tissue, shivering, thermoregulatory behaviors, and dermal vasomotor control will be analyzed to
understand the physiology and the importance of implementing techniques to promote thermoregulation
and survival in the critical post-birth period of mammals. Also, infrared thermography as
a helpful method to perform thermal measurements without animal interactions does not affect
these parameters.Non
The effects of dietary crude protein level on ammonia emissions from slurry from lactating Holstein-Friesian cows as measured in open-circuit respiration chambers.
Get PDFPublication history: Accepted - 10 May 2022; Published online - 12 May 2022The effect of dietary crude protein (CP) level on ammonia (NH3) emissions from slurry from lactating Holstein-Friesian cows was studied. Twenty-four-hour total collections of faeces and urine were made from 24 lactating Holstein-Friesian cows fed four total mixed rations containing 141, 151, 177, and 201 g CP/kg DM (6 cows/diet). The collected urine and faeces from each cow were combined to form 2 kg duplicate slurry samples (weight/weight; fresh basis) according to the proportions in which they were excreted. NH3 emissions from the slurry samples were measured, during 0–24 and 24–48 h intervals in six open-circuit respiration chambers maintained at two temperatures (8 or 18 °C). NH3 emissions for the 0–24 and 0–48 h intervals, as well as the average daily emissions, increased linearly with increasing dietary CP level. Increasing the temperature from 8 to 18 °C positively affected NH3 emissions, but only for the 0–24 h interval. In situations where direct measurements are impossible, NH3 emissions from slurry can be predicted accurately using equations based on dietary CP level supported by either urinary nitrogen, faeces nitrogen, or both. In summary, increasing dietary CP level linearly increased average daily NH3 emissions from slurry, with a 5.4 g increase for each 10 g increase in dietary CP.This research project was funded by the Department of Agriculture Environment and Rural Affairs (DAERA) in Northern Ireland