Prediction of milk yield using visual images of cows through deep learning.

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg.The broad objective of the study was to determine, through deep learning, the predictability of milk yield from a cow's image data. The data size of 1238 image pairs (the side-view images and the rear-view images) from 743 Holstein cows within their first or second parity and the cows’ corresponding first lactation 305-day milk yield values were used to train a deep learning model. The data was first split into the training and testing data at the ratio of 80:20, respectively. The training data was then augmented four times more, then again split into training and validation data at the ratio of 80:20, respectively. Three principal analyses were done, i.e. the prediction of milk yield using rear-view images only, the prediction of milk yield using the side-view images only and the prediction of milk yield using a merge of the side-view and rear-view images (the combined-view images). In all three analyses, poor predictions were observed, i.e. R2 values of 0.32 for the model using the side-view image, 0.30 for the model using the rear-view images and 0.38 for the model using combined side and rear images. The mean absolute errors were 1146.4 kg, 1148.3 kg and 1112.9 kg for the side-view, the rear-view and the combined-view models, respectively. The root mean square error values were 1460.7 kg, 1480.5 kg and 1401.2 kg and the mean absolute error percentages were 17.6, 17.3 and 17.0 % for the side-view, rear-view and combined-view models, respectively. Hypotheses tests were also done to check whether there was any difference between these three prediction models. There was no significant difference in performance between all the prediction models (p>0.05), i.e. the side-view model, the rear-view model and the combinedview model. It was concluded that predicting 305-day milk yield of Holstein cows using either view has the same level of accuracy and no additional benefits are derived from using both the rear and the side views. Keywords: Computer vision; deep learning; linear conformation traits; 305-day milk yield; side-view images; rear-view images; combined-view images; Holstein cows

Assessing the predictive value of dairy facial biometrics for measures of productivity, health, and social dominance

Includes bibliographical references.2018 Fall.To view the abstract, please see the full text of the document

The effect of selection for milk yield on milk flow and udder measurements

Data were collected from the Iowa State University Research Farm at Ankeny, Iowa. The objectives of this study were: (1) to investigate the correlated responses in milk flow, udder and teat measurements to selecting sires for high and average milk production, (2) to find estimates of heritability and repeatability of these measurements, (3) to examine their relationship with udder health and milk production, and (4) to investigate the relationship of teat-end classification with udder health, lactation milk yield, and milk flow. The realized differences in milk production due to selection adjusted for the year of calving were 1275 lb. for foundation cows, and 2525, 2637, and 2843 lb. for progeny of high minus average sires in generations one, two, and three, respectively;Progeny of high sires had a significantly higher average rate of milk flow, and maximum rate than progeny of average sires in generation one; higher initial rate, 2-min milk, average rate, and maximum rate in generation two; and higher 2-min milk, average rate, and maximum rate in generation three. Cows, lactations, and year-seasons had significant effects on measurements of milk flow. Estimates of repeatability for measurements of milk flow ranged from .22-.47 and estimates of heritability ranged from .13-.26. Phenotypic correlations indicated that high yielders had faster rates of milk flow and higher incidences of mastitis;Selection for higher milk yield caused udders to be closer to the ground, closer to the hock, and to have greater distances between teats pre- and postmilking. Cows and lactations had significant effects on udder and teat measurements. Estimates of repeatability for udder and teat measurements ranged from .27-.75 and estimates of heritability ranged from .52-.70. Lactation milk yield had negative phenotypic correlations with udder height and depth of cleft and positive correlations with total distances between teats. Low udders, greater distances between teats, and longer teats were associated with higher incidences of mastitis;Funnel followed by plate teat-end shapes had higher clinical mastitis cases than other shapes. Round teat ends were associated with slower rate of milk flow while plate-shaped teat ends were associated with faster rate of milk flow

Identification and Assessment of Lameness in Sows Through the Utilization of NUtrack AND GAITFour Systems

Lameness is a financial concern for producers and a welfare concern for the animals. Utilizing both the GAITFour and NUtrack systems, gilts’ natural tendencies and gait were analyzed to better understand the onset of lameness and what indicators can be identified in a commercial setting. Beginning at 20 weeks of age, video on replacement gilts was collected for 9 consecutive days and processed using the NUtrack System to identify individual gilts’ distance travelled (m), avg speed (m/s), angle rotated (degrees), and time standing (s), sitting (s), eating (s), and laying (s). NUtrack is a deep learning-based multi-object tracking system that has been shown to achieve greater than 92.5% precision and recall when tracking the long-term location and identity of individual pigs in group-housed settings. At the start of evaluation under the NUtrack system, gilts were walked across a pressure sensing mat (GAITFour system) to evaluate the gait metrics of Step Length (cm), Stride Length (cm), Swing Percent of Cycle, Swing Time (sec), Stance Percent of Cycle, Stance Time (sec), Total Scaled Pressure (TSP), GAITFOURDog Lameness Score (GLS), Total Pressure Index (TPI), and Step/Stride ratio. A total of 3,150 replacement gilts were analyzed utilizing the data derived from NUtrack with 1,379 gilts culled based on structural unsoundness as determined by an experienced herdsman. A subset totaling 2,634 gilts were analyzed utilizing the data derived from GAITFour with 1,199 being culled primarily based on structural unsoundness as determined by an experienced herdsman. Heritability estimates were done on novel objective measurements that can be utilized for gilt selection for increased sow longevity. For the NUtrack system, heritabilities are 0.14±0.0069, 0.14±0.0074, 0.31±0.0418, 0.35±0.0425, 0.32±0.0420, 0.30±0.0409, 0.21±0.0359, 0.22±0.0370, and 0.23±0.0372 for angle, average speed, distance, eat, lie lateral, lie sternal, lie total, sit, and stand respectively. Average speed (p\u3c0.001) and time standing (p\u3c0.01) were significantly associated with gilt retention. For the GAITFour system, heritability estimates ranged from 0.03 to 0.36. Step length of both the left and right front legs (p\u3c0.001), stride length of both the left and right front legs (p\u3c0.01), stance time of the right front leg (p\u3c0.05), total scaled pressure of the right hind leg (p\u3c0.05), step/stride ratio of both the left and right front legs (p\u3c0.001), and step/stride ratio of the left hind leg (p\u3c0.05) were all found to be significantly associated with gilt retention. As a result of this project, we aim to increase the selection of sound replacement females in order to decrease the progression of lameness. Advisor: Benny E. Mot

RNAi-mediated Reduction of a Major Ruminant Specific Milk Allergen Using a Transgenic Mouse Model

Milk from dairy cows is an important human food. It contains the protein beta-lactoglobulin (BLG) which is not present in human milk and thought to be a major allergen in the milk of cows. RNA interference (RNAi), mediated by sequence-specific micro RNAs (miRNAs), provides a new molecular tool to reduce the levels of undesirable proteins. In this study, I have screened ten miRNAs targeting the BLG mRNA for their potential to knockdown BLG expression using a cell-based in vitro assay. I identified four miRNAs which showed substantial bovine BLG (bBLG) (78-97%) and ovine BLG (oBLG) (33-94%) knockdown activity in vitro. Tandem miRNA constructs with combinations of these four single miRNAs did not result in significantly increased knockdown efficiency compared to the respective single miRNA constructs in the in vitro assay (P>0.05). Because targeting of two different regions has the potential for greater knockdown efficiency in vivo, I chose a tandem construct which achieved in vitro up to 99% bBLG knockdown as compared to 92% and 74% of bBLG knockdown by the single miRNAs. The tandem construct also showed 90% of oBLG knockdown in comparison to 92% and 69% of oBLG knockdown by the single miRNAs in the in vitro assay which made it an ideal candidate for the subsequent evaluation in transgenic (Tg) mice. For the in vivo studies, the cytomegalovirus (CMV) promoter of the selected miRNA constructs was replaced with the promoter of the mouse milk protein gene for whey acid protein (WAP) which directs the expression of the BLG-specific miRNAs to the lactating mammary gland. The Tg mouse lines generated with the tissue-specific tandem construct and the single miRNAs used for the tandem miRNA construct were then crossed with an oBLG or bBLG expressing Tg mouse line to generate double transgenic (miRNA-BLG) mice for assessing BLG knockdown in vivo. Analysis of the milk proteins demonstrated that the tandem miRNA reduced the levels of oBLG and bBLG in milk from the miRNA-BLG mice up to 96% and 46%, respectively. This study validates the mammary gland specific expression of miRNAs as a promising approach to knockdown allergenic proteins in milk

The perception and relief of pain associated with lameness in dairy cattle.

SIGLEAvailable from British Library Document Supply Centre-DSC:DXN024009 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Studies on the body composition of beef cows

Suckler cow management systems generally require cows to be dependent on their body reserves of energy and protein at some stage of the production cycle. In nutritional studies with suckler cows it is therefore important that the rate of use or replenishment of body reserves be considered with contemporary nutrition. This requires the quantification of body reserves and hence a means of measuring body composition in the live animal.The methods available for the estimation of in vivo body composition in animals are reviewed and a number of techniques (live weight, skeletal size, total body water as estimated by deuterium oxide dilution, blood and red cell volumes as estimated by Evans Blue dilution, ultrasonic measurement of subcutaneous fat depth and eye-muscle area, and body condition scoring) were examined using 73 non-pregnant, non-lactating cows of five genotypes (Hereford x Friesian, Blue-Grey, Galloway, Luing and British Friesian) ranging in body condition score from 0.75-4.5. Direct measurement of body composition in terms of water, fat, protein and ash were made following slaughter.Live weight, deuterium oxide dilution, ultrasonic measurement of subcutaneous fat depth and eye-muscle area, and body condition scoring were all considered to be potentially useful predictors of body composition, but a combination of techniques offered a better prediction than did any single index. Using a combination of techniques it was possible to predict body fat and protein with residual standard deviations of 13.1 kg and 3.15 kg respectively.Body composition changes were also examined, and it was calculated that the composition of empty body-weight change was dependent upon empty body weight, containing more fat and less water, protein and ash at higher empty body weights.Important breed differences were found in the partition of fat among the main adipose tissue depots, with the Friesian cows having a greater proportion of fat in the internal depots and a lower proportion in the subcutaneous depot. The implications of breed differences in fat partition are discussed in relation to in vivo body composition measurement.An ancillary study was carried out into the effects of body condition on maintenance requirements and on the use of blood metabolites to measure energy status in suckler cows. This indicated that body condition affected maintenance requirements to the extent that at 500 kg live weight, maintenance requirements were 8 MJ ME/day less for each unit increase in condition score. Plasma free fatty acids were shown to be particularly useful in assessing energy status in cows, but 3-hydroxybutyrate concentrations were of little value in non-pregnant, non-lactating animals.Finally, the conclusions of the two studies are discussed in relation to areas of study likely to prove useful in the development of efficient systems of suckled calf production

The dairy herd health and productivity service

Herd health and reproduction have been ranked as top priorities for improving the future productivity and profitability of dairy enterprises. There is a multitude of genetic, disease, nutritional, management and physiological issues that can dramatically alter health and reproduction. It is generally agreed that a multidisciplinary approach is necessary if improvement is to be achieved. Herd health schemes have evolved in the dairy industry throughout the world but the uptake of such schemes in the UK has been low. The veterinary input to many dairy farms is at best routine fertility visits confined to examination of the reproductive tract, and at worst occasional emergency calls. The Dairy Herd Health and Productivity Service (DHHPS) was established to provide the opportunity for veterinary surgeons to lead a multidisciplinary team which can monitor health, fertility and production and can plan remedial action, when necessary. Over a period of twenty years it has continued to identify infertility, mastitis and lameness as the main reasons for the involuntary disposal of dairy cows, although on some farms BSE has been a major factor. The trend in the last few years has been for an increase in culling for reasons of disease rather than for age or yield. The average disease rates have remained consistently high with over 100 treatments per 100 cows each year. Infertility, mastitis and lameness are the most common disease problems on DHHPS farms.Blood profiling and condition scoring have demonstrated that at least a third of cows tested were mobilising excessive fat during the transition from the dry period to early lactation. The DHHPS found 34.3% of 9,235 dry cows, sampled 0- 14 days before calving and 28 per cent of 20,502 cows between 5-40 days post calving, had raised BHB blood concentrations. 30.6 per cent of the same dry cows and 21.9 per cent of the early lactation animals had elevated NEFA results.Blood urea was measured to reflect the current protein intake and the protein /energy balance of the ration. 14 per cent of 9325 dry cows and 9.5 per cent of 20502 of early lactation cows had low urea N (<1.7 mmol/1). 25 per cent of the cows sampled between 5-40 days post partum had blood urea nitrogen concentrations above 3.3mmol/l.Low magnesium levels were detected throughout the year. 9.2 per cent of 9235 dry cows and 7 per cent of 19,738 early lactation cows between 5-40 days calved had blood magnesium concentration <0.8 mmol/1.GSHPx was used as an indicator of selenium status. 16.3 per cent of 1,206 heifers and 4.9 per cent of 6,998 cows had low GSHPx results Metabolic profiling can assist in identifying possible nutritional imbalances, but is likely to be most effective when it is carried out as part of a full, systematic investigation of the nutritional status of the herd.A survey of farmers and veterinary surgeons who have been involved with DHHPS indicated that they are receiving considerable benefits from the service. The service, by combining techniques such as computerised data recording and pre-planned blood analysis, provides regular information on disease occurrence, adequacy of nutrition and management in relation to productivity and economic performance. The main reason for its success was the team approach. The DHHPS has facilitated the solving of complex problems by encouraging multidisciplinary participation and affords the opportunity for the veterinary practitioner to become involved in giving positive advice on animal health

Mechatronics applications and prototyping sensors for the precision livestock farming

The study is subdivided into 5 chapters and comprises a review of the main components of Plf, the development of a prototype for EC monitoring in ewe milk, a prototype for monitoring animals body temperature, the optimization of collection rounds of goat milk and the development of a prototype for somatic cell count (SCC) through the measurement of Sodium ions in ewe milk.‬‬‬ The first chapter is a review of the advancements of the main components of Plf, i.e. software, hardware and data transmission, focusing on issues related to hardware modularity and differences between licensed and unlicensed software. From the review it emerges that image processing is one of the most used techniques in Plf systems, in that it allows the detection of behavioral, biological and pathological parameters without interfering with the animals routine activities. In this regard the area occupied by a lamb carcass was calculated by using an image analysis open source software, CellProfiler (Jones et al., 2008). The second chapter deals with the realization of an innovative portable tool for somatic cells count in ewe milk by measuring its electrical conductivity. There are over 15,000 dairy sheep farms in Sardinia, which represent both historically and economically the most important agricultural and livestock sector in the island. Indeed, Sardinia holds more than 40% of the national sheep population thanks to more than 3 million sheep heads that provide about 60% of the total national milk production. One of the most common problems in sheep farms is mastitis, an intramammary infection which may cause a quantitative reduction up to 50% in milk production and a qualitative drop, in particular of lactose and casein. One of the indirect methods for the assessment of somatic cell count (SCC) in ruminants’ milk is through the measurement of its electrical conductivity (EC). In small ruminants, EC has a reasonable correlation R2 = 0.35 with somatic cells but to date there is still not a portable tool that can estimate SCC based on the milk’s EC reading. The prototype was calibrated on Sarda ewe milk. The aim of Chapter 3 was to develop a system using a open source sensors, actuators and micro-controller. The system is able to monitoring the rectal temperature of the animals, sending data via Bluetooth to a smart phone. The micro-controller used was an ATmega32U4, the temperature was read using the LM35 analogic sensor and a Class 1 Bluetooth serial module was connected to Arduino creating a wireless serial link between an Android phone and the Arduino board. The application for receiving data on an android smart phone was created using App Inventor that is an innovative Android application creation software developed by Massachusetts Institute of Technology (MIT). This app is free available on Google Play Store under the name animal_temp. The costs of sheep milk collection rounds in Sardinia have been analysed in chapter fourth. The escalating costs incurred by the dairy processing industries for milk collection from individual farms have focused the attention on the rationalization of milk collection and transport systems. In this regard, the case of the Sardinian goat sector has characteristics that make it unique and not comparable to other logistics optimization realities. The problems of this sector are mainly represented by the particular conditions of the rural road network and the fragmented nature of livestock farms. The aim of the present study was to test a milk collection route optimization software, MilkTour, in the collection rounds of a sample cheese dairy. The software has been developed by the Land Engineering Section of the Agriculture Department of the University of Sassari. A total of 5 routes were analysed and optimized. The results have highlighted the importance of optimizing collection routes as they have a significant impact on business costs. A important contribution that has emerged is the strong correlation between collection density and the cost per litre of collected milk (€cent/l), which allows to detects the cost-effectiveness of a round of collection and its relative optimized around. The objective of chapter 5 was to study the relationship between the ione Na+ and the main components of sheep milk, in particular somatic cells. Moreover, a portable device for estimating SCC in sheep milk was designed. The study was conducted on over 2000 samples. The milk components examined were: fat, proteins, lactose, pH, sodium chloride, urea and the ions Na+. The correlation between Na + and SCC corresponded to R2 = 0.76 (P &lt;0.01). The prototype developed incorporates two containers which receives milk samples taken from each half udder. Each container has integrated inside two sensors, one to detect the level of Na+ in the milk and the other one to compensate the milk temperature. The mathematical model, loaded into the microcontroller by a firmware written in C / C ++, analyze the data and gives back the estimate of SCC level, so it allows farmers to monitor the ewes health status by periodically comparing the somatic cell counts of each half udder. While dealing with different topics the 5 chapters can be enclose in a big new topic, called Precision Livestock Farming (Plf). Plf is the discipline that allows to monitor in real-time the numerous biological and environmental parameters concerning each individual animal of the herd. A Plf system is always made up by three components: a physical element, i.e. the hardware; an element for data processing and presentation, known as the software; and an element for the transmission of data, i.e. the network. The hardware comprises the sensors, the computers and/or microcontrollers, the data transmission and acquisition systems and the actuators. Mathematical models for data processing and the data presentation interface are included in the software loaded into the microcontroller