Multi-Pig Part Detection and Association with a Fully-Convolutional Network

Computer vision systems have the potential to provide automated, non-invasive monitoring of livestock animals, however, the lack of public datasets with well-defined targets and evaluation metrics presents a significant challenge for researchers. Consequently, existing solutions often focus on achieving task-specific objectives using relatively small, private datasets. This work introduces a new dataset and method for instance-level detection of multiple pigs in group-housed environments. The method uses a single fully-convolutional neural network to detect the location and orientation of each animal, where both body part locations and pairwise associations are represented in the image space. Accompanying this method is a new dataset containing 2000 annotated images with 24,842 individually annotated pigs from 17 different locations. The proposed method achieves over 99% precision and over 96% recall when detecting pigs in environments previously seen by the network during training. To evaluate the robustness of the trained network, it is also tested on environments and lighting conditions unseen in the training set, where it achieves 91% precision and 67% recall. The dataset is publicly available for download

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 \u3c 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

Extracellular vesicles: pathogenic messengers and potential therapy for neonatal lung diseases

Extracellular vesicles (EVs) are a heterogeneous group of nano-sized membranous structures increasingly recognized as mediators of intercellular and inter-organ communication. EVs contain a cargo of proteins, lipids and nucleic acids, and their cargo composition is highly dependent on the biological function of the parental cells. Their cargo is protected from the extracellular environment by the phospholipid membrane, thus allowing for safe transport and delivery of their intact cargo to nearby or distant target cells, resulting in modification of the target cell's gene expression, signaling pathways and overall function. The highly selective, sophisticated network through which EVs facilitate cell signaling and modulate cellular processes make studying EVs a major focus of interest in understanding various biological functions and mechanisms of disease. Tracheal aspirate EV-miRNA profiling has been suggested as a potential biomarker for respiratory outcome in preterm infants and there is strong preclinical evidence showing that EVs released from stem cells protect the developing lung from the deleterious effects of hyperoxia and infection. This article will review the role of EVs as pathogenic messengers, biomarkers, and potential therapies for neonatal lung diseases

Topoisomerase I copy number alterations as biomarker for irinotecan efficacy in metastatic colorectal cancer

BACKGROUND: No biomarker exists to guide the optimal choice of chemotherapy for patients with metastatic colorectal cancer. We examined the copy numbers (CN) of topoisomerase I (TOP1) as well as the ratios of TOP1/CEN-20 and TOP1/CEN-2 as biomarkers for irinotecan efficacy in patients with metastatic colorectal cancer. METHODS: From a national cohort, we identified 163 patients treated every third week with irinotecan 350 mg/m(2) as second-line therapy. Among these 108 were eligible for analyses and thus entered the study. Primary tumors samples were collected and tissue microarray (TMA) blocks were produced. FISH analysis was performed using two probe-mixes: TOP1/CEN-20 and TOP1/CEN-2. Only samples harboring all three signals (TOP1, CEN-20 and CEN-2) using FISH were included in the analyses. RESULTS: In the TOP1/CEN-20 probe-mix the median TOP1- and CEN-20 CN were 4.46 (range: 1.5–9.5) and 2.00 (range: 0.55–4.55), respectively. The median TOP1- and CEN-2 CN in the TOP1/CEN-2 probe-mix, were 4.57 (range: 1.82–10.43) and 1.98 (range: 1.22–6.14), respectively. The median TOP1/CEN-20 ratio and TOP1/CEN-2 ratio were 1.25 (range: 0.92–2.90) and 2.05 (range: 1.00–6.00), respectively. None of the markers TOP1 CN, TOP1/CEN-20-ratio or TOP1/CEN-2-ratio were associated with progression free survival, overall survival or baseline characteristics. Yet, we observed a borderline association for a stepwise increase of the TOP1 CN in relation to objective response as hazard ratio were 1.35 (95% CI 0.96–1.90; p = 0.081). CONCLUSIONS: We verified a borderline significant association between increasing TOP1 CN and objective response as previously reported. Applying the probes representing CEN-20 and CEN-2, in order to investigate the ratios of TOP1/CEN-20 and TOP1/CEN-2 provided no further information in search of a biomarker driven patient stratification. Other biomarkers to be paired with TOP1 CN are therefore highly warranted

Evaluation of Precision Livestock Technology and Human Scoring of Nursery Pigs in a Controlled Immune Challenge Experiment

The objectives were to determine the sensitivity, specificity, and cutoff values of a visual-based precision livestock technology (NUtrack), and determine the sensitivity and specificity of sickness score data collected with the live observation by trained human observers. At weaning, pigs (n = 192; gilts and barrows) were randomly assigned to one of twelve pens (16/pen) and treatments were randomly assigned to pens. Sham-pen pigs all received subcutaneous saline (3 mL). For LPS-pen pigs, all pigs received subcutaneous lipopolysaccharide (LPS; 300 µg/kg BW; E. coli O111:B4; in 3 mL of saline). For the last treatment, eight pigs were randomly assigned to receive LPS, and the other eight were sham (same methods as above; half-and-half pens). Human data from the day of the challenge presented high true positive and low false positive rates (88.5% sensitivity; 85.4% specificity; 0.871 Area Under Curve, AUC), however, these values declined when half-and-half pigs were scored (75% sensitivity; 65.5% specificity; 0.703 AUC). Precision technology measures had excellent AUC, sensitivity, and specificity for the first 72 h after treatment and AUC values were \u3e0.970, regardless of pen treatment. These results indicate that precision technology has a greater potential for identifying pigs during a natural infectious disease event than trained professionals using timepoint sampling