Estimating genetic parameters of digital behavior traits and their relationship with production traits in purebred pigs

BACKGROUND

With the introduction of digital phenotyping and high-throughput data, traits that were previously difficult or impossible to measure directly have become easily accessible, offering the opportunity to enhance the efficiency and rate of genetic gain in animal production. It is of interest to assess how behavioral traits are indirectly related to the production traits during the performance testing period. The aim of this study was to assess the quality of behavior data extracted from day-wise video recordings and estimate the genetic parameters of behavior traits and their phenotypic and genetic correlations with production traits in pigs. Behavior was recorded for 70 days after on-test at about 10 weeks of age and ended at off-test for 2008 female purebred pigs, totaling 119,812 day-wise records. Behavior traits included time spent eating, drinking, laterally lying, sternally lying, sitting, standing, and meters of distance traveled. A quality control procedure was created for algorithm training and adjustment, standardizing recording hours, removing culled animals, and filtering unrealistic records.

RESULTS

Production traits included average daily gain (ADG), back fat thickness (BF), and loin depth (LD). Single-trait linear models were used to estimate heritabilities of the behavior traits and two-trait linear models were used to estimate genetic correlations between behavior and production traits. The results indicated that all behavior traits are heritable, with heritability estimates ranging from 0.19 to 0.57, and showed low-to-moderate phenotypic and genetic correlations with production traits. Two-trait linear models were also used to compare traits at different intervals of the recording period. To analyze the redundancies in behavior data during the recording period, the averages of various recording time intervals for the behavior and production traits were compared. Overall, the average of the 55- to 68-day recording interval had the strongest phenotypic and genetic correlation estimates with the production traits.

CONCLUSIONS

Digital phenotyping is a new and low-cost method to record behavior phenotypes, but thorough data cleaning procedures are needed. Evaluating behavioral traits at different time intervals offers a deeper insight into their changes throughout the growth periods and their relationship with production traits, which may be recorded at a less frequent basis.

Evaluation of a novel computer vision-based livestock monitoring system to identify and track specific behaviors of individual nursery pigs within a group-housed environment

Animal behavior is indicative of health status and changes in behavior can indicate health issues (i.e., illness, stress, or injury). Currently, human observation (HO) is the only method for detecting behavior changes that may indicate problems in group-housed pigs. While HO is effective, limitations exist. Limitations include HO being time consuming, HO obfuscates natural behaviors, and it is not possible to maintain continuous HO. To address these limitations, a computer vision platform (NUtrack) was developed to identify (ID) and continuously monitor specific behaviors of group-housed pigs on an individual basis. The objectives of this study were to evaluate the capabilities of the NUtrack system and evaluate changes in behavior patterns over time of group-housed nursery pigs. The NUtrack system was installed above four nursery pens to monitor the behavior of 28 newly weaned pigs during a 42-d nursery period. Pigs were stratified by sex, litter, and randomly assigned to one of two pens (14 pigs/pen) for the first 22 d. On day 23, pigs were split into four pens (7 pigs/pen). To evaluate the NUtrack system’s capabilities, 800 video frames containing 11,200 individual observations were randomly selected across the nursery period. Each frame was visually evaluated to verify the NUtrack system’s accuracy for ID and classification of behavior. The NUtrack system achieved an overall accuracy for ID of 95.6%. This accuracy for ID was 93.5% during the first 22 d and increased (P < 0.001) to 98.2% for the final 20 d. Of the ID errors, 72.2% were due to mislabeled ID and 27.8% were due to loss of ID. The NUtrack system classified lying, standing, walking, at the feeder (ATF), and at the waterer (ATW) behaviors accurately at a rate of 98.7%, 89.7%, 88.5%, 95.6%, and 79.9%, respectively. Behavior data indicated that the time budget for lying, standing, and walking in nursery pigs was 77.7% ± 1.6%, 8.5% ± 1.1%, and 2.9% ± 0.4%, respectively. In addition, behavior data indicated that nursery pigs spent 9.9% ± 1.7% and 1.0% ± 0.3% time ATF and ATW, respectively. Results suggest that the NUtrack system can detect, identify, maintain ID, and classify specific behavior of group-housed nursery pigs for the duration of the 42-d nursery period. Overall, results suggest that, with continued research, the NUtrack system may provide a viable real-time precision livestock tool with the ability to assist producers in monitoring behaviors and potential changes in the behavior of group-housed pigs.

130 Utilization of Nutrack to Assess Variance Components and Heritability of Activity Traits

Overall activity and behavior are integral components of sows remaining productive in the herd. This investigation studied overall activity of group housed replacement gilts and the heritability of various activity traits. Beginning around 20 wk of age, video recorded data of approximately 75 gilts/group for a total of 2,378 gilts over 32 groups was collected for 7 consecutive d using the NUtrack System, which tracks distance travelled (m), avg speed (m/s), angle rotated (degrees), and time standing (s), sitting (s), eating (s), and laying (s). The recorded phenotypes were standardized to the distribution observed within a pen for each group. The final values used for analysis were the average daily standardized values. Data were analyzed using mixed models (RStudio V 1.2.5033) including effects of sire, dam, dam’s sire and dam, dam’s grandsire and granddam, farrowing group, barn, pen, and on-test date. Sire had an effect on every activity trait P < 0.001), and dam had an effect on average speed (P < 0.001). The dam’s sire had an effect on all activity traits (P < 0.001) and the dam’s grandsire had an effect on average speed (P < 0.001). Heritabilities and variance components of activity traits were estimated in ASReml 4 using an animal model with a two-generation pedigree. Genetic variances are 0.17 +/- 0.029, 0.19 +/- 0.034, and 0.11 +/- 0.024, residual variances are 0.37 +/- 0.023, 0.41 +/- 0.027, and 0.41 +/- 0.022, phenotypic variances are 0.54 +/- 0.018, 0.60 +/- 0.020, and 0.52 +/- 0.016, and heritabilities are 0.32 +/- 0.048, 0.32 +/- 0.049, and 0.21 +/- 0.044 for average speed, distance, and lie respectively. NUtrack offers potential to aid in selection decisions. Given the results presented herein, continued investigation into these activity traits and their association with sow longevity is warranted.

42 Activity and Bone Lesion Analysis on Gilt Retention to the Breeding Herd

A consistent theme in swine production is to increase efficiency and reduce input costs. In this study, sow activity traits and lesions were analyzed to identify associations with lameness and gilt retention. Gilts (n = 73) were culled based on structural unsoundness as determined by an experienced herdsman. Females (n = 132) that had been retained for breeding, but either did not show estrus at an appropriate age or were excessed due to limited farrowing space were used as controls. Gilts were recorded with the NUtrack System for 1 week prior to selection. The NUtrack System records distance travelled (m), time standing (s), eating (s), and laying (s), angle rotated (degrees) and average speed (m/s). Animals were humanely harvested in a USDA inspected abattoir. Both ends of the humerus and the femur head were evaluated for osteochondrosis or osteoarthritis lesions. Joint lesions were categorized as Major or Minor lesions. Major lesions were severe osteochondrosis lesions where cartilage was severely fractured or cartilage exhibited a region of necrosis larger than 2 millimeters in diameter. Minor lesions were defined creases or indentations in the cartilage or where abnormal blood flow existed in bone tissue underneath cartilage. Ninety-eight animals were identified with minor or major lesions (28 cull and 70 control). Unexpectedly, chi-square analysis did identify control animals as having higher incidences of minor or major lesions than cull animals (p < 0.05). Data were analyzed using logistic regression (RStudio V1.2.5033) with farrowing group included in the model. No NUtrack trait was predictive of joint lesions (P > 0.1). However, time standing (P < 0.001) and average speed (P < 0.05) were significantly associated with being retained for breeding. These data suggest that animal behavior and movement, as analyzed by NUtrack, can enhance herdsman efforts in making culling decisions of breeding animals.

181 Utilization of the Nutrack Livestock Monitoring System to Identify Changes in General and Spatial Behaviors of Newly Weaned Nursery Exposed to an Endotoxin Challenge

Incorporation of precision livestock technology has the potential to provide swine producers with the means to rapidly and accurately identify immune-compromised pigs, allowing for accurate and timely interventions. The objective of this study was to utilize the NUtrack System (NUtrack) to identify changes in general (lying, standing and sitting) and spatial behaviors (at the feeder and meters/day) of newly weaned pigs exposed to a lipopolysaccharide (LPS) challenge. To achieve this objective, 12 nursery pens with 192 weaned pigs (16 pigs/pen) were randomly assigned to three treatments (4 pens/treatment): Control (saline injection), Mixed (8 pigs/pen received an LPS challenge and 8 pigs received saline injection) and 100% (all pigs received LPS). The LPS challenge consisted of a bolus subcutaneous injection at 300 µg/kg BW (E. coli O111:B4). Prior to placement, NUtrack was installed above the 12 nursery pens and initiated continuous data capture for the duration of the nursery phase (43 days). Ten days after placement in the nursery pens pigs received the assigned challenge (LPS or sham). Data were analyzed using the MIXED procedure of SAS specific for repeated measures (SAS Inst. Inc., Cary, NC). Regardless of treatment group, general special behaviors were similar (P = >0.28) prior to the LPS challenge (days 1–9). Following LPS challenge (day 10), spatial behaviors decreased (P = <0.01) and time associated with general behaviors increased (P = <0.01) for LPS challenged pigs when compared to pigs not challenged (Control and 50% non-challenged). This change in both general and spatial behaviors remained until day 12. In addition, general and spatial behaviors of the 50% treatment (challenged and non-challenged) were different (P = < 0.03), when compared to Controls. Results suggest precision livestock technology, like the NUtrack System, has the potential to monitor changes in behaviors following an endotoxin challenge.

End-Effector Contact and Force Detection for Miniature Autonomous Robots Performing Lunar and Expeditionary Surgery

INTRODUCTION

The U.S. Space Force was stood up on December 20, 2019 as an independent branch under the Air Force consisting of about 16,000 active duty and civilian personnel focused singularly on space. In addition to the Space Force, the plans by NASA and private industry for exploration-class long-duration missions to the moon, near-earth asteroids, and Mars makes semi-independent medical capability in space a priority. Current practice for space-based medicine is limited and relies on a "life-raft" scenario for emergencies. Discussions by working groups on military space-based medicine include placing a Role III equivalent facility in a lunar surface station. Surgical capability is a key requirement for that facility.

MATERIALS AND METHODS

To prepare for the eventuality of surgery in space, it is necessary to develop low-mass, low power, mini-surgical robots, which could serve as a celestial replacement for existing terrestrial robots. The current study focused on developing semi-autonomous capability in surgical robotics, specifically related to task automation. Two categories for end-effector tissue interaction were developed: Visual feedback from the robot to detect tissue contact, and motor current waveform measurements to detect contact force.

RESULTS

Using a pixel-to-pixel deep neural network to train, we were able to achieve an accuracy of nearly 90% for contact/no-contact detection. Large torques were predicted well by a trained long short-term memory recursive network, but the technique did not predict small torques well.

CONCLUSION

Surgical capability on long-duration missions will require human/machine teaming with semi-autonomous surgical robots. Our existing small, lightweight, low-power miniature robots perform multiple essential tasks in one design including hemostasis, fluid management, suturing for traumatic wounds, and are fully insertable for internal surgical procedures. To prepare for the inevitable eventuality of an emergency surgery in space, it is essential that automated surgical robot capabilities be developed.

Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.

PSVIII-22 Utilization of NUtrack to assess sire influence on pig activity and activity effects on weight

Structural conformation and behavior are integral components in sows remaining productive in the herd. This initial investigation studied the impact of activity data on weight and the impact of sires on overall activity of group housed replacement gilts. Beginning at 19 wk of age, video recorded data of approximately 75 gilts/wk for a total of 230 gilts over 3 wk was collected for 7 consecutive d using the NUtrack system, which tracks distance travelled (m), time standing (s), eating (s), and laying (s), and angle rotated (degrees). Any d that logged for less than 24 hr were dropped from analysis. Data were analyzed using mixed models (SAS V 9.4) including random effects of dam, barn, pen, and on-test date, and fixed effects including total laying time, angle rotated, distance travelled, time standing, and sire. For 20 wk wt, the mixed model included distance, laying, angle, and standing. Sire had an effect on distance traveled (P < 0.05). The following traits also had an effect on distance: angle (P < 0.01), laying (P < 0.001), standing (P < 0.001), sitting (P < 0.01), and eating (P < 0.01). Pearson correlation coefficient showed a positive correlation between wt and laying (0.26), and negative correlations between wt and distance (-0.34), standing (-0.28) and angle (-0.42). The regression of distance on 20 wk wt yielded a regression coefficient of -0.027 (P < 0.05) m/d per lb and the model explained 11.85% of the variation in 20 wk wt. NUtrack can be utilized to track activities and distance travelled of swine in group pens. Given the results presented herein, continued investigation into the heritability of these activity traits and their association with sow longevity is warranted.

Using Visual and Digital Imagery to Quantify Horn Fly (Diptera: Muscidae) Densities

The horn fly, Haematobia irritans L. (Diptera: Muscidae), is a persistent pest of cattle globally. A threshold of 200 flies per animal is considered the standard management goal; however, determining when that threshold has been exceeded is difficult using visual estimates that tend to overestimate the actual fly densities and are, at best, subjective. As a result, a more reliable and durable method of determining horn fly densities is needed. Here, we describe the methods commonly used to quantify horn fly densities including visual estimates and digital photography, and provide examples of quantification software and the prospect for computer automation methods.

3 Deep Frame-based tracking on nursery pigs

Rapid identification of morbid/injured pigs is essential for swine producers to ensure the health and well-being of each individual pig and ensure production efficiency. As such, there is a need to develop advanced technology as a means to further ensure the health and well-being of pigs. The objective of this study was to evaluate a novel computer vision, Deep-Frame – Detection and Tracking Platform (DF–DTP), for the ability to automatically identify/maintain identity and continuously track the activities of group-housed pigs. Utilizing a depth-enabled camera and multi-ellipsoid expectation maximization technology, 28 nursery pigs were continuously evaluated during the first 42 d of the nursery phase. Over the 42-d nursery period, the DF–DTP was capable of achieving a 93.7% accuracy for identifying and maintaining the identity of individual pigs. Through visual validation (10,544 observations), 642 identification errors were detected. Of the identification errors, 82% occurred when pigs were lying, 7.8% standing, 2.1% walking, 7.2% at the feeder (at the feeder), and 1.0% at the waterer. The DF–DTP was capable of a 96.2% accuracy rate for classification of an individual pig’s activity. Accuracy for classification of activities was 96.3% for walking, 96.3 for standing, 99.1 for lying, 86.4% for at the feeder, and 73.6% for at the waterer. Across the 42-d trial, the average time pigs spent 77.8% (+ 0.02) lying, 8.6% (+ 0.32) standing, 2.9% (+ 0.09) walking and traveled 943.1 meters/d (+ 195.9). Over time (d 1 – d 42), the time pigs spent lying, standing, walking, and meters/d decreased (P 0.001). As d within the nursery phase increased, time at the feeder increased (P < 0.001), there was no change (P = 0.11) for time at the waterer. Results of the study indicate that the DF–DTP is capable of accurately identifying, maintaining the identity of and continuously tracking the activity of group-housed nursery pigs.

Stereoscopic vision-based robotic manipulator extraction method for enhanced soft tissue reconstruction

The availability of digital stereoscopic video feedback on surgical robotic platforms allows for a variety of enhancements through the application of computer vision. Several of these enhancements, such as augmented reality and semi-automated surgery, benefit significantly from identification of the robotic manipulators within the field of view. A method is presented for the extraction of robotic manipulators from stereoscopic views of the operating field that uses a combination of marker tracking, inverse kinematics, and computer rendering. This method is shown to accurately identify the locations of the manipulators within the views. It is further demonstrated that this method can be used to enhance 3D reconstruction of the operating field and produce augmented views.

A compact high-definition low-cost digital stereoscopic video camera for rapid robotic surgery development

Robotic surgical platforms require vision feedback systems, which often consist of low-resolution, expensive, single-imager analog cameras. These systems are retooled for 3D display by simply doubling the cameras and outboard control units. Here, a fully-integrated digital stereoscopic video camera employing high-definition sensors and a class-compliant USB video interface is presented. This system can be used with low-cost PC hardware and consumer-level 3D displays for tele-medical surgical applications including military medical support, disaster relief, and space exploration.

Stereo image-based arm tracking for in vivo surgical robotics

Motor-based tracking and image-based tracking are considered for three-dimensional in vivo tracking of the arms of a surgical robot during minimally invasive surgery. Accurate tracking is necessary for tele-medical applications and for the future automation of surgical procedures. An experiment is performed to compare the accuracy of the two methods, and results show that the positioning error of image-based tracking is significantly less than that of motor-based tracking.