The development and assessment of novel non-invasive methods of measuring sleep in dairy cows : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatū, New Zealand

Onet published article in Appendix C was removed for copyright reasons, but may be accessed via its source: Hunter, L.B., O’Connor, C., Haskell, M.J., Langford, F.M., Webster, J.R., & Stafford, K.J. 2021, September. Lying posture does not accurately indicate sleep stage in dairy cows. Applied Animal Behaviour Science, 242, 105427. https://doi.org/10.1016/j.applanim.2021.105427Sleep is important for animal health and welfare and there are many factors, for example, the environment, illness, or stress, that are likely to have an impact on cow sleep and consequently affect their welfare. Polysomnography (PSG) is considered the gold standard for precise identification of sleep stages. It consists of electrophysiological recordings of the brain activity, eye movements and muscle activity but is costly and difficult to use with cows on farm. Accordingly, the study of sleep in cows may be limited due to the impracticability of PSG. Alternative methods of assessing sleep have been developed for humans. Some such work has been conducted for cows, but this has yet to be validated with PSG. The main aim of this thesis was to investigate alternative methods to PSG to accurately detect sleep stages in dairy cows. Specifically, I aimed to develop a detailed 5-stage scoring system for assessing sleep stages from the cow PSG, to investigate the suitability of using lying postures and heart rate (HR) measures to assess sleep stages and to develop a model to accurately predict sleep stages using non-invasive measures in dairy cows compared with PSG. Two studies were conducted using 6 non-lactating dairy cows in an indoor housed environment in Scotland, and outdoors at pasture in New Zealand. PSG was recorded with each cow over a period of seven days. From these data a 5-stage sleep-scoring criteria with good reliability was developed which identified two stages of light sleep, two stages of deep sleep as well as awake and rumination stages. Video was recorded during sleep recordings and the cow’s behaviour was analysed and compared with the scored sleep stages from the PSG. Some sleep stages were found to occur mainly in specific lying postures; however, overall, postures were not useful indicators of sleep stages. Heart rate (HR) and heart rate variability (HRV) were measured using a Polar HR monitor ii and data logging device. Differences in the HR and HRV measures were found between the sleep stages, and the patterns of these changes were similar between both Scottish and NZ cows. Finally, machine learning models were developed using supervised learning methods to predict sleep stage from the HR and HRV measures as well as the surface EMG data recorded during PSG. The models were able to learn to recognize and accurately predict sleep stages compared with the PSG scoring. This research demonstrates that non-invasive alternatives can be used to identify sleep stages accurately in dairy cows compared with PSG. Further research is necessary with larger sample sizes and cows of various breeds and life stages; however, the success of the methods developed during this thesis demonstrates their suitability for the future measurement of sleep in cows and in the assessment of cow welfare

Nesting and nighttime behaviours of captive chimpanzees (Pan troglodytes)

Abstract Studies of nesting behaviours of free-ranging apes typically focus on ecological variables such as preferred tree species and areas within the home range, heights of nests, and nest group sizes. However, nesting in captive apes is rarely studied, despite the ubiquity of this sleep-related behaviour. The paucity of field data is often attributed to the inherent difficulty in observing what is essentially a nighttime behaviour. Captive settings can provide researchers with an ideal opportunity to record nesting and sleep-related behaviours, yet such research on captive apes is also scant. Topics addressed include current practices in zoos regarding conditions for sleep in great apes, the potential effects of social and environmental factors on sleep site selection, the motor patterns involved in nest construction, preferred nesting structures and substrates, and nocturnal behaviours. This thesis documented and empirically tested hypotheses concerning nest-related activities in captive chimpanzees, with an aim to generate practical recommendations for enclosure design, sleeping areas, sleeping structures, and nesting substrates that have implications for the welfare of captive apes. As with the few reports that already exist, most chimpanzees in this research frequently constructed night nests. When building a nest, some techniques appeared to be universal across individuals and groups, where others were group-specific or occasionally characteristic of only certain individuals. An experiment showed that specific materials are preferred over others for nest building. Many chimpanzees appeared to express persistent preferences for particular sleeping sites, and for some this was to maintain proximity to kin or other closely bonded individuals. In one group, individual sleeping site preferences changed across seasons, although again this was subject to individual differences. Video analyses of nighttime behaviours demonstrated that, although nests/sleep sites are primarily used for rest subsequent to retirement, a number of social and non-social activities were performed throughout the night. In conjunction with analysis of postural and orientation shifts, these data are unique in describing the nocturnal behaviours of chimpanzees out with a laboratory setting. Several aspects of nest-related behaviours showed a high degree of inter-and intra-group variation. Although this cautions against generalising findings across captive populations, research of this type has applied implications for the management of captive ape species, and can add to our as-yet meagre understanding of their nest and sleep-related behaviours

Effects of Acute Lying and Sleep Deprivation on the Behavior and Immune Function of Lactating Dairy cows

The objective of the study was to determine the effects of sleep or lying deprivation on the behavior, production, metabolism and immune function of dairy cows. Data were collected from 8 multi- and 4 primi-parous cows (DIM = 199 ± 44 (mean ± SD); days pregnant = 77 ± 30). Each cow experienced: 1) 24 h sleep deprivation implemented by noise or physical contact and 2) 24 h lying deprivation imposed by a wooden grid placed on the pen floor that prevented a recumbent position. An 11-d collection period (from 2 d before the first treatment (trt) to 8 d after trt) was followed by 12-d washout periods. Study days were organized from 2100 to 2059. During habituation (d -2 and -1 before trt), baseline (d 0), and trt (d 1), housing was individual stalls (mattress with no bedding). After trt, cows returned to sand-bedded freestalls for a 7-d recovery period (d 2 to 8). Lying behaviors were recorded by accelerometers attached to the hind leg. Milk yield was recorded 2× daily. NEFA and glucose concentrations were evaluated from serum sampled at 0300, 0900, 1500, and 2100 on d 1 and 2. Data were analyzed using a mixed model in SAS including fixed effects of trt, day, and their interaction with significant main effects separated using a PDIFF statement (P ≤ 0.05). Lying time decreased during trt and increased on the first day of recovery for lying deprivation compared to sleep deprivation (d 1: 1.9 vs. 8.4 ± 0.7 h/d (mean ± pooled SE); P \u3c 0.001; d 2: 16.8 vs. 13.6 ± 0.7 h/d; P = 0.002). Milk yield decreased during lying deprivation compared to sleep (P = 0.002). NEFA and glucose varied by time (P ≤ 0.03). IL-1β and TNF-α were higher during trt, compared to baseline for both treatments (day: P = 0.04 and P = 0.004, respectively). Collectively, this suggests, lack of access to resting resources rather than the relative comfort of that resource, may have greater long-term effects on the welfare of dairy cows

Resting behaviour of dairy cows: applications to farm assurance and welfare

Lying is a restful, high priority behaviour for dairy cows which can be affected by various factors associated with production but is not directly related to productivity. As such, lying behaviour has potential for use as an indicator of welfare. Information in the literature regarding the effect of stage of lactation on lying behaviour was contradictory and information on optimum lying behaviour and maximum bout lengths was scarce. The aim of this study was to improve knowledge in these areas and find a way of using lying behaviour to assess welfare. Pregnant heifers were observed at pasture in order to describe lying behaviour in conditions that may be considered optimum. Lying behaviour at pasture was characterised as having 10.5 h total lying time per 24h, few (6-7) lying bouts and a long maximum bout length (3.5h). The effect of two very different levels of production on the lying behaviour of heifers during their first lactation and housing period was compared. Although total lying times did not change much over the lactation, early location was associated with disturbed lying behaviour (increased lying frequency and short bout lengths) and indicators of metabolic challenge in low input heifers. High input heifers however, showed more disturbance later in lactation associated with being moved to another feeding group. Two pilot studies were carried out to investigate cows' preferences for cubicles with mats or mattresses and to compare lying behaviour on the two surfaces. Social factors appeared to affect preference and lying behaviour. Consequently total lying times were very low (less than 8h) and preferences were not clear. However, lying times were low even in a group of undisturbed late lactation cows and the pattern of lying (number of bouts and maximum bout length) was similar to that of heifers at grass

The Effects of Pair versus Individual Housing Preweaned Dairy Calves on Behavior, Growth, and Acquired Immunity

Our objective was to determine the effect of pair versus individual housing of calves on growth, behavior, and immunity. At 5 ± 1 d relative to birth, calves with successful passive transfer of immunoglobulins from colostrum were blocked by sex and birth date. Housing treatment was assigned to either pair (n = 14) or individual (n =14) housing. Calf pairing was implemented by combining two individual pens. One paired calf served as the focal calf and the other imposed treatment. All data were collected from the focal calf in pair housing. Control calves remained individually housed. ADG, DM, feed refusals, and growth at weaning to one-week-post weaning did not differ between housing treatments. Paired calves spent more time awake, and increased standing time. Individual calves projected their head out of the pen more frequently. Hunger and anticipation behaviors did not differ between housing treatments. These data suggest paired calves were more active during the milk feeding stage. The increased activity of pair housed calves may suggest improved welfare of preweaned calves. IgG and IgM ELISA units to keyhole limpet heomocyanin did not differ between housing treatments. IgG ELISA units at d 14 were lower than d 3, 28, and 35 in all calves. IgM ELISA units were highest at d 3, but continued to drop thereafter. The stimulation index for delayed hypersensitivity to Candida albicans did not differ between housing treatments. However, they did increased over time, and peaked at 24 and 48 h post C. albicans injections. Pain sensitivity did not differ between housing treatments, however calves increased sensitivity at 27, 51, and 75 h, relative to disbudding. Pair housing dairy calves during the preweaned period did not negatively affect the immune development of dairy calves or pain from disbudding. This suggests social housing calves early in life does not suppress the immune system, or increase pain sensitivity after disbudding

Animal Welfare Assessment

This Special Issue provides a collection of recent research and reviews that investigate many areas of welfare assessment, such as novel approaches and technologies used to evaluate the welfare of farmed, captive, or wild animals. Research in this Special Issue includes welfare assessment related to pilot whales, finishing pigs, commercial turkey flocks, and dairy goats; the use of sensors or wearable technologies, such as heart rate monitors to assess sleep in dairy cows, ear tag sensors, and machine learning to assess commercial pig behaviour; non-invasive measures, such as video monitoring of behaviour, computer vision to analyse video footage of red foxes, remote camera traps of free-roaming wild horses, infrared thermography of effort and sport recovery in sport horses; telomere length and regulatory genes as novel biomarkers of stress in broiler chickens; the effect of environment on growth physiology and behaviour of laboratory rare minnows and housing system on anxiety, stress, fear, and immune function of laying hens; and discussions of natural behaviour in farm animal welfare and maintaining health, welfare, and productivity of commercial pig herds

The Effect of Straw on the Behaviour of Sows in Tether Stalls

The behaviour of sows in tether stalls with and without straw was studied in two experiments. Sows lay down more when 1 kg of straw was provided daily, especially when it was chopped and mixed wet with the food (dietary effect). Sows without straw performed a variety of stereotyped oral and other activities which were greatly reduced by the provision of loose straw that could be chewed and manipulated throughout the day (recreational effect). Sows were frequently seen standing or sitting motionless with the head drooping, probably in a state of drowsiness. This behaviour was virtually eliminated by full straw bedding (bedding effect). Certain \u27comfort movements\u27, bar-biting at feeding time, and biting the neighbouring sows, were not influenced by straw. It is concluded that the dietary, recreational and bedding aspects of straw are all significant, but influence different aspects of the animals\u27 behaviour. The significance of bar-biting and other activities is discussed

Behavioural and electrophysiological characterisation of sleep in sheep and its application in animal welfare studies

Major aims in the study of animal welfare are to try and understand the subjective mental experience of animals, to develop methods to assess their responses to changes in mental state and to use this information to enhance animal welfare. One of the most profound changes of mental state observable in all mammals is the change between wakefulness and sleep. Electrophysiological measurements, when combined with behavioural observations, provide a powerful means of characterising the states of sleep and wakefulness of animals. The spectral components of an electroencephalogram (EEG) reflect the differences in the electrical activity of the brain between sleep and wakefulness.When humans undergo an aversive, stressful, disturbing, or worrying experience during wakefulness, their subsequent sleep can be affected. The present series of investigations examined the hypothesis that sheep exposed to aversive husbandry procedures would experience disturbances to their subsequent sleep. A sleep disturbance might provide an indication of the effect of an aversive husbandry procedure on the mental state of a sheep, that would not otherwise have been detected using conventional methods such as behavioural observation, blood biochemistry and heart rate.Non-invasive electrophysiological hardware and software developed and used for human sleep studies, was adapted and used to study sleep in sheep. To assess the effectiveness of surface electrophysiological recordings to detect changes in the electrical activity of the brain of a sheep, three validation studies were carried out. They consisted of a) the post-mortem passage of electrical current through the head of a sheep; b) changes in EEG in response to depth of general anaesthesia and c) the EEG responses of a sheep in a sleep posture to an auditory stimulus.The method was then applied to characterise the sleep of six, housed, adult ewes. Three percent (± 0.2) of a 24-h period was spent in rapid-eye-movement (REM) sleep and 15% (± 2.4) was spent in Non-REM sleep.Three experiments were undertaken to assess the effects of potentially aversive husbandry procedures on subsequent sleep. These consisted of a) movement to a novel environment; b) an 8-h road transport journey and c) a 29-h space Thesis Abstract restriction period (simulating times and space allowances used during road transport). Changes were seen in the distribution, quality and quantity of sleep. Although there were no significant effects on the duration of REM sleep or NonREM sleep, in two experiments, an increase in the number of REM sleep bouts was seen post-treatment. In all experiments, a post-treatment increase in the percentage of slow waves was seen in Non-REM sleep.This work provided a greater understanding of the impact of potentially aversive husbandry procedures on rest and sleep in sheep. All three of the potentially aversive husbandry procedures used as experimental treatments were associated with changes in subsequent sleep that may have been indicative of aversive experience during wakefulness. Although the changes in sleep found post-treatment were not large, they were consistent and reliable and therefore the methodology has potential for use in other applied animal welfare studies

Physical workload and musculoskeletal symptoms in the human-horse work environment

Most work in horse stables is performed manually in much the same way as a century ago, with old-fashioned tools and equipment. It is one of the least mechanised sectors dealing with large animals, which often involves work in awkward postures and lifts of heavy loads. However, there is a lack of knowledge of the ergonomic risks in the human-horse work environment. This thesis seeks to provide a deeper understanding of the human-horse work environment, work tasks, workload and frequency of musculoskeletal symptoms and to identify potential risk factors for the development of musculoskeletal symptoms. Self-reporting methods (questionnaires, rating scales), observation methods (OWAS, REBA), descriptive task analysis (HTA, HA, GTS) and biomechanical analysis (JACK) were used to collect and analyse data. Riding instructors surveyed in the questionnaire study reported high levels of perceived musculoskeletal symptoms in at least one of nine anatomical areas during the past year and the past week. The most frequently reported problem areas were the shoulders, the lower back and the neck. Mucking out stables was considered to be the task involving the heaviest work. OWAS analysis showed that three work tasks contained a high proportion of unacceptably awkward work postures, namely mucking out, preparing bedding and sweeping. During mucking out and sweeping, the back was bent and twisted for most of the time. There were many high-risk operations involved in mucking out boxes and disposing of bedding material. Emptying a wheel barrow on the muck heap included high-risk operations with awkward postures such as twisted, bent back arms over shoulder level and handling high loads. The analytical methods used clearly revealed where in the work tasks the ergonomic problems occurred. In almost all operations with a high risk level, a shafted tool or wheelbarrow was used. Analysis of the shaft length of two hand-held tools used for mucking out (manure fork, shavings fork) showed that the manure fork should have a longer shaft to reduce loading on the back. The results for the shavings fork were inconclusive, but indicated the importance of changes in work technique. More in-depth knowledge of the musculoskeletal symptoms and work tasks performed in the human-horse work environment makes it easier to plan and implement measures to prevent musculoskeletal symptoms in this particular group of workers