Automatic Lameness Detection in a Milking Robot : Instrumentation, measurement software, algorithms for data analysis and a neural network model

The aim of this thesis is to develop a fully automatic lameness detection system that operates in a milking robot. The instrumentation, measurement software, algorithms for data analysis and a neural network model for lameness detection were developed. Automatic milking has become a common practice in dairy husbandry, and in the year 2006 about 4000 farms worldwide used over 6000 milking robots. There is a worldwide movement with the objective of fully automating every process from feeding to milking. Increase in automation is a consequence of increasing farm sizes, the demand for more efficient production and the growth of labour costs. As the level of automation increases, the time that the cattle keeper uses for monitoring animals often decreases. This has created a need for systems for automatically monitoring the health of farm animals. The popularity of milking robots also offers a new and unique possibility to monitor animals in a single confined space up to four times daily. Lameness is a crucial welfare issue in the modern dairy industry. Limb disorders cause serious welfare, health and economic problems especially in loose housing of cattle. Lameness causes losses in milk production and leads to early culling of animals. These costs could be reduced with early identification and treatment. At present, only a few methods for automatically detecting lameness have been developed, and the most common methods used for lameness detection and assessment are various visual locomotion scoring systems. The problem with locomotion scoring is that it needs experience to be conducted properly, it is labour intensive as an on-farm method and the results are subjective. A four balance system for measuring the leg load distribution of dairy cows during milking in order to detect lameness was developed and set up in the University of Helsinki Research farm Suitia. The leg weights of 73 cows were successfully recorded during almost 10,000 robotic milkings over a period of 5 months. The cows were locomotion scored weekly, and the lame cows were inspected clinically for hoof lesions. Unsuccessful measurements, caused by cows standing outside the balances, were removed from the data with a special algorithm, and the mean leg loads and the number of kicks during milking was calculated. In order to develop an expert system to automatically detect lameness cases, a model was needed. A probabilistic neural network (PNN) classifier model was chosen for the task. The data was divided in two parts and 5,074 measurements from 37 cows were used to train the model. The operation of the model was evaluated for its ability to detect lameness in the validating dataset, which had 4,868 measurements from 36 cows. The model was able to classify 96% of the measurements correctly as sound or lame cows, and 100% of the lameness cases in the validation data were identified. The number of measurements causing false alarms was 1.1%. The developed model has the potential to be used for on-farm decision support and can be used in a real-time lameness monitoring system.

Design and assessment of weirs for fish passage under drowned conditions

In aquatic systems, in-stream structures such as dams, weirs and road crossings can act as barriers to fish movement along waterways. There is a growing array of technological fish-pass solutions for the movement of fish across large structures such as weirs and dams. However, most existing weir structures lack dedicated fishways, and fish often have to rely on drowned conditions to move upstream. In order to assess the adequacy of a given or proposed weir for upstream fish passage under drowned conditions, it is necessary to determine, firstly, the hydraulic properties of the drowned weir with respect to the requirements of the fish community and, secondly, the duration and timing of drowning flows with respect to the hydrograph for the site and the likely timing of fish movements. This paper primarily addresses the first issue. A computer program has been developed and incorporated in a simple-to-operate spreadsheet for the determination of the hydraulic characteristics of a drowned weir which are important to fish movement. The program is based on a theoretical analysis of drowned weirs and subsequent extensive verification in laboratory experiments. Inputs to the program include site information comprising channel cross-section data, channel slope, and channel roughness, and weir information comprising weir height and the required minimum drowned depth over the weir for migrating fish passage. The program then calculates the flow rate at which the required level of drowning occurs, the velocity characteristics above the weir (including transverse distributions), and flow depths and velocities upstream and downstream of the weir. The paper discusses (briefly) the theoretical background of the program and its experimental verification. A case study is then presented that illustrates the use of the program in the field to assess fish passage opportunities at an existing weir and to develop a case for retrofitting a fishway. Some discussion is also provided on the contribution of a modelled drownout volume to the assessment of how significant a barrier a weir is to fish passage. It is shown that the program is an important new additional tool in the assessment of the adequacy of weir structures in providing for fish movement and informing associated fish passage solutions. (C) 2011 Elsevier B.V. All rights reserved.

Natural outbreak of Streptococcus agalactiae (GBS) infection in wild giant Queensland grouper, Epinephelus lanceolatus (Bloch), and other wild fish in northern Queensland, Australia

Ninety-three giant Queensland grouper, Epinephelus lanceolatus (Bloch), were found dead in Queensland, Australia, from 2007 to 2011. Most dead fish occurred in northern Queensland, with a peak of mortalities in Cairns in June 2008. In 2009, sick wild fish including giant sea catfish, Arius thalassinus (Ruppell), and javelin grunter, Pomadasys kaakan (Cuvier), also occurred in Cairns. In 2009 and 2010, two disease epizootics involving wild stingrays occurred at Sea World marine aquarium. Necropsy, histopathology, bacteriology and PCR determined that the cause of deaths of 12 giant Queensland grouper, three wild fish, six estuary rays, Dasyatis fluviorum (Ogilby), one mangrove whipray, Himantura granulata (Macleay), and one eastern shovelnose ray, Aptychotrema rostrata (Shaw), was Streptococcus agalactiae septicaemia. Biochemical testing of 34 S.agalactiae isolates from giant Queensland grouper, wild fish and stingrays showed all had identical biochemical profiles. The 16S rRNA gene sequences of isolates confirmed all isolates were S.agalactiae; genotyping of selected S.agalactiae isolates showed the isolates from giant Queensland grouper were serotype Ib, whereas isolates from wild fish and stingrays closely resembled serotype II. This is the first report of S.agalactiae from wild giant Queensland grouper and other wild tropical fish and stingray species in Queensland, Australia.

Fish mediate high food web connectivity in the lower reaches of a tropical floodplain river

High levels of hydrological connectivity during seasonal flooding provide significant opportunities for movements of fish between rivers and their floodplains, estuaries and the sea, possibly mediating food web subsidies among habitats. To determine the degree of utilisation of food sources from different habitats in a tropical river with a short floodplain inundation duration (similar to 2 months), stable isotope ratios in fishes and their available food were measured from three habitats (inundated floodplain, dry season freshwater, coastal marine) in the lower reaches of the Mitchell River, Queensland (Australia). Floodplain food sources constituted the majority of the diet of large-bodied fishes (barramundi Lates calcarifer, catfish Neoarius graeffei) captured on the floodplain in the wet season and for gonadal tissues of a common herbivorous fish (gizzard shad Nematalosa come), the latter suggesting that critical reproductive phases are fuelled by floodplain production. Floodplain food sources also subsidised barramundi from the recreational fishery in adjacent coastal and estuarine areas, and the broader fish community from a freshwater lagoon. These findings highlight the importance of the floodplain in supporting the production of large fishes in spite of the episodic nature and relatively short duration of inundation compared to large river floodplains of humid tropical regions. They also illustrate the high degree of food web connectivity mediated by mobile fish in this system in the absence of human modification, and point to the potential consequences of water resource development that may reduce or eliminate hydrological connectivity between the river and its floodplain.

Demonstration reaches: Looking back whilst moving forward with river rehabilitation under the Native Fish Strategy

‘Demonstration reaches’ are sections of river where multiple threats to native fish are addressed through river rehabilitation and strong community participation. They are an important way of promoting the key driving actions of the Murray-Darling Basin Authority's Native Fish Strategy (NFS) by using on-ground community-driven rehabilitation. Measuring rehabilitation success against well-defined targets and using this information to adaptively mange activities is fundamental to the demonstration reach philosophy. Seven years on from the establishment of the first demonstration reach, there are now seven throughout the Murray-Darling Basin (MDB), all in differing states of maturation and but all applying a standardised framework for monitoring native fish outcomes. In this study, we reflect on the role that demonstration reaches have played within the NFS, synthesise some key findings from 32 monitoring and evaluation outputs, and highlight some of the successes and barriers to success. We make recommendations as to how to strengthen the demonstration reach model to ensure it remains a relevant approach for fish habitat rehabilitation beyond the NFS and MDB.

Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies. © 2013.

Elevated CO2 affects the behavior of an ecologically and economically important coral reef fish

We tested the effect of near-future CO2 levels (a parts per thousand 490, 570, 700, and 960 mu atm CO2) on the olfactory responses and activity levels of juvenile coral trout, Plectropomus leopardus, a piscivorous reef fish that is also one of the most important fisheries species on the Great Barrier Reef, Australia. Juvenile coral trout reared for 4 weeks at 570 mu atm CO2 exhibited similar sensory responses and behaviors to juveniles reared at 490 mu atm CO2 (control). In contrast, juveniles reared at 700 and 960 mu atm CO2 exhibited dramatically altered sensory function and behaviors. At these higher CO2 concentrations, juveniles became attracted to the odor of potential predators, as has been observed in other reef fishes. They were more active, spent less time in shelter, ventured further from shelter, and were bolder than fish reared at 490 or 570 mu atm CO2. These results demonstrate that behavioral impairment of coral trout is unlikely if pCO(2) remains below 600 mu atm; however, at higher levels, there are significant impacts on juvenile performance that are likely to affect survival and energy budgets, with consequences for predator-prey interactions and commercial fisheries.

Micro-economic drivers of profitability in an ITQ-managed fishery: An analysis of the Queensland Coral Reef Fin-Fish Fishery

An economic survey of the commercial operators currently active in the Queensland Coral Reef Fin-Fish Fishery has been carried out, as part of a research project aimed at evaluating alternative management options for this fishery. This paper presents the background analysis used as a basis to develop the sampling design for this survey. The background analysis focuses on activity patterns of the fleet based on effort and catch information, as well as patterns of quota ownership. Based on this information, a fishing business profile describing the micro-economic structure of fishing operations is developed. This profile, in conjunction with the qualitative information gained in undertaking the economic surveys, allows preliminary understanding of the key drivers of profitability in the CRFFF, and possible impacts of external factors on fishing operations.

Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish

Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr : Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L–1) of the freshwater resulted in the Sr : Ca being substantially higher than the marine water. Importantly, the otolith Sr : Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr : Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr : Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element : Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr : Ca alone can be problematic without an understanding of water chemistry.

Revolutionising Fish Ageing: Using Near Infrared Spectroscopy to Age Fish

The project aimed to evaluate the innovative application of NIRS as a reliable, repeatable, and cost-effective method of ageing fish, using otoliths of Barramundi and Snapper as study species. Specific research questions included assessing how geographic and seasonal variation in otoliths affects NIRS predictive models of fish age, as well as how the NIR spectra of otoliths change in the short-term (i.e., <12 months) and long-term (i.e., historical otolith collections) and what effect this has on the predictive ability of NIRS models. The cost-effectiveness of using NIRS to supplement standard fish ageing methods was also evaluated using a hypothetical case study of Barramundi.

Improving Profitability to Industry Through the Identification and Management of 'tough' Fish Syndrome in Tropical Saddletail Snapper (Lutjanus Malabaricus)

OBJECTIVES: 1. To determine whether incomplete rigor mortis resolution and 'cold shock' play a role in development of tough fish syndrome (TFS) in tropical Saddletail snapper. 2. To identify links between TFS and specific physiological factors in tropical Saddletail snapper. 3. Communicate findings and recommendations to stakeholders and assist with implementation of any changes to fishing or handling practices required.

Fish Silage as Replacement of Fishmeal in Red Tilapia Feeds

We estimated the effect on growth and nutrient efficiency of replacing fishmeal with silage incorporated with rice bran in diets for fingerling red tilapia (Oreochromis mossambicus × Oreochromis niloticus × Oreochromis aureus) over 12 weeks. Isonitrogenous (300 g kg−1 protein dry matter basis) and isoenergetic (4450 Kcal gross energy kg−1) feed formulations with increasing levels of tilapia silage as a replacement for fishmeal were prepared: Diet 1 with no silage (0 g Kg−1), Diet 2 (250 g Kg−1), Diet 3 (500 g Kg−1), and Diet 4 (750 g Kg−1). Feed intake was similar among Diets 1, 2, and 3, while Diet 4 had a significantly lower intake. There was no significant difference (P > 0.05) in weight gain or specific growth rate (SGR), feed conversion ratio (FCR), and protein efficiency ratio (PER), among fish fed Diets 1, 2, and 3. Fish fed with Diet 4 had significantly lower weight gain; SGR and PER and significantly higher FCR. Organoleptic properties of the fish were not affected by the diets. The results of this study indicate that less expensive dried fish silage with rice bran is an alternative protein source for tilapia feed up to 50% of fishmeal replacement.