Learning end-to-end respiratory rate prediction of dairy cows from RGB videos.

Respiratory rate (RR) is an important indicator of the health and welfare status of dairy cows. In recent years, progress has been made in monitoring the RR of dairy cows using video data and learning methods. However, existing approaches often involve multiple processing modules, such as region of interest (ROI) detection and tracking, which can introduce errors that propagate through successive steps. The objective of this study was to develop an end-to-end computer vision method to predict RR of dairy cows continuously and automatically. The method leverages the capabilities of a state-of-the-art Transformer model, VideoMAE, which divides video frames into patches as input tokens, enabling the automated selection and featurization of relevant regions, such as a cow's abdomen, for predicting RR. The original encoder of VideoMAE was retained, and a classification head was added on top of it. Further, the weights of the first 11 layers of the pre-trained model were kept, while the weights of the final layer and classifier were fine-tuned using video data collected in a tie-stall barn from 6 dairy cows. Respiratory rates measured using a respiratory belt for individual cows were serving as the ground truth (GT). The evaluation of the developed model was conducted using multiple metrics, including mean absolute error (MAE) of 2.58 breaths per minute (bpm), root mean squared error (RMSE) of 3.52 bpm, root mean squared prediction error (RMSPE; as a proportion of observed mean) of 15.03%, and Pearson correlation (r) of 0.86. Compared with a conventional method involving multiple processing modules, the end-to-end approach performed better in terms of MAE, RMSE and RMSPE. These results suggest the potential to implement the developed computer vision method for an end-to-end solution, for monitoring RR of dairy cows automatically in a tie-stall setting. Future research on integrating this method with other behavioral detection and animal identification algorithms for animal monitoring in a free-stall dairy barn can be beneficial for a broader application.

Exhalomics as a noninvasive method for assessing rumen fermentation in dairy cows: Can exhaled-breath metabolomics replace rumen sampling?

Previously, we used secondary electrospray ionization-mass spectrometry (SESI-MS) to investigate the diurnal patterns and signal intensities of exhaled (EX) volatile fatty acids (VFA) of dairy cows. The current study aimed to validate the potential of an exhalomics approach for evaluating rumen fermentation. The experiment was conducted in a switchback design, with 3 periods of 9 d each, including 7 d for adaptation and 2 d for sampling. Four rumen-cannulated original Swiss Brown (Braunvieh) cows were randomly assigned to 1 of 2 diet sequences (ABA or BAB): (A) low starch (LS; 6.31% starch on a dry matter basis) and (B) high starch (HS; 16.2% starch on a dry matter basis). Feeding was once per day at 0830 h. Exhalome (with the GreenFeed System), and rumen samples were collected 8 times to represent every 3 h of a day, and EX-VFA and ruminal (RM)-VFA were analyzed using SESI-MS and HPLC, respectively. Furthermore, the VFA concentration in the gas phase (HR-VFA) was predicted based on RM-VFA and Henry's Law (HR) constants. No interactions were identified between the types of diets (HS vs. LS) and the measurement methods on daily average VFA profiles (RM vs. EX or HR vs. EX), suggesting a consistent performance among the methods. Additionally, when the 3-h interval VFA data from HS and LS diets were analyzed separately, no interactions were observed between methods and time of day, indicating that the relative daily pattern of VFA molar proportions was similar regardless of the VFA measurement method used. The results revealed that the levels of acetate sharply increased immediately after feeding, trailed by an increase in the acetate:propionate ratio and a steady increase for propionate (2 h after feeding the HS diet, 4 h for LS), and butyrate. This change was more pronounced for the HS diet than the LS diet. However, there was no overall diet effect on the VFA molar proportions, although the measurement methods affected the molar proportions. Furthermore, we observed a strong positive correlation between the levels of RM and EX acetate for both diets (HS: r = 0.84; LS: r = 0.85), RM and EX propionate (r = 0.74), and RM and EX acetate:propionate ratio (r = 0.80). Both EX-VFA and RM-VFA exhibited similar responses to feeding and dietary treatments, suggesting that EX-VFA could serve as a useful proxy for characterizing RM-VFA molar proportions to evaluate rumen fermentation. Similar relationships were observed between RM-VFA and HR-VFA. In conclusion, this study underscores the potential of exhalomics as a reliable approach for assessing rumen fermentation. Moving forward, research should further explore the depth of exhalomics in ruminant studies to provide a comprehensive insight into rumen fermentation metabolites, especially across diverse dietary conditions.

Evaluating GreenFeed and respiration chambers for daily and intraday measurements of enteric gaseous exchange in dairy cows housed in tie-stalls.

The objective of this study was to evaluate the GreenFeed (GF) and respiration chambers (RC) for daily and intraday measurements of the enteric gaseous exchange, as well as the metabolic heat production, lying behavior, and feed intake (FI) rate of dairy cows at these 2 respective housing conditions [tie-stall barn (TS) vs. RC] during the summer periods. Sixteen multiparous lactating dairy cows were recruited and arranged in a randomized complete block design with a baseline period established for each cow. Cows were given a basal diet (CON) for a baseline period of 7 d and were then fed a 3-nitrooxypropanol (3-NOP)-containing feed for the subsequent 26 d as experimental period. During both the baseline and the last 7 d of treatment period, gaseous exchanges of each animal were measured in the TS using GF for 8 6-hourly staggered measurements over 3 d, immediately followed by the measurement in RC for 2 d. Corresponding DMI, milk yield, and behavior parameters (e.g., lying behavior and FI rate) in TS and RC were recorded. The correlation coefficients of CH4 and H2 using raw data were 0.84 and 0.85, respectively. For all gases, correlation coefficients between GF and RC on individual cow level decreased when the marginal fixed effects (e.g., inhibitor and breed) were corrected by a mixed model. There were no differences in daily CH4 production or intensity between GF and RC (442 vs. 443 g CH4/d or 16.6 vs. 16.2 g CH4 /kg MY). However, greater CH4 yield was measured by GF than RC (19.0 vs. 17.8 g CH4/kg DMI), driven by a lower DMI (23.3 vs. 24.6 kg/d) when cows were housed in TS sampled by GF compared with cows being housed and sampled in RC. The correlations for CO2 production and O2 consumption were moderate and expected due to the variation associated with the mild heat stress condition during GF measurements in the TS (Thermal humidity index (THI) 56 vs. 68), as indicated by the reduced lying time (-2.1 h/d). At the intraday level, there was an interaction between techniques and hour-of-day for CH4 production, as indicated by the discrepancies in post-prandial CH4 emissions between techniques. In summary, this set of results showed that there were strong positive correlations for CH4 and H2 emissions between GF and RC based on individual cow data. However, such relationship should be interpreted with caution, given the data clustering resulting from the use of inhibitor 3-NOP. On treatment level, these 2 techniques detected similar inhibitor effect on the estimated daily CH4 emissions. The intraday patterns of CH4 and H2 production captured by GF provided a close approximation for those measured by RC. Nevertheless, potential underestimation may occur, especially following fresh feed delivery. For measuring CO2 production and O2 consumption, the GF captured similar intraday variations to those in the RC. However, the estimated daily production and consumption were not directly comparable, which was expected due to the variable thermal conditions during the summer. Further evaluations under the same weather conditions are warranted.

Effects of 3-nitrooxypropanol (Bovaer10) and whole cottonseed on milk production and enteric methane emissions from dairy cows under Swiss management conditions.

The objective of this study was to determine the potential effect and interaction of 3-nitrooxypropanol (3-NOP; Bovaer, DSM-Firmenich Nutrition Products Ltd.) and whole cottonseed (WCS) on lactational performance and enteric methane (CH4) emission of dairy cows. A total of 16 multiparous cows, including 8 Holstein Friesian (HF) and 8 Brown Swiss (BS; 224 ± 36 DIM, 26 ± 3.7 kg milk yield, mean ± SD), were used in a split-plot design, where the main plot was the breed of cows. Within each subplot, cows were randomly assigned to a treatment sequence in a replicated 4 × 4 Latin square design with 2 × 2 factorial arrangements of treatments with four 24-d periods. The experimental treatments were as follows: (1) control (basal TMR), (2) 3-NOP (60 mg/kg TMR DM), (3) WCS (5% TMR DM), and (4) 3-NOP + WCS. The treatment diets were balanced for ether extract, crude protein, and NDF contents (4%, 16%, and 43% of TMR DM, respectively). The basal diets were fed twice daily at 0800 and 1800 h. Dry matter intake and milk yield were measured daily, and enteric gas emissions were measured (using the GreenFeed System, C-Lock Inc.) during the last 3 d of each 24-d experimental period when animals were housed in tiestalls. There was no difference in DMI on treatment level, whereas the WCS treatment increased ECM yield and milk fat yield. No interaction of 3-NOP and WCS occurred for any of the enteric gas emission parameters, but 3-NOP decreased CH4 production (g/d), CH4 yield (g/kg DMI), and CH4 intensity (g/kg ECM) by 13%, 14%, and 13%, respectively. Further, an unexpected interaction of breed by 3-NOP was observed for different enteric CH4 emission metrics: HF cows had a greater CH4 mitigation effect compared with BS cows for CH4 production (g/d; 18% vs. 8%), CH4 intensity (g/kg milk yield; 19% vs. 3%), and CH4 intensity (g/kg ECM; 19% vs. 4%). Hydrogen production was increased by 2.85-fold in HF and 1.53-fold in BS cows receiving 3-NOP. Further, a 3-NOP × time interaction occurred for both breeds. In BS cows, 3-NOP tended to reduce CH4 production by 18% at approximately 4 h after morning feeding, but no effect was observed at other time points. In HF cows, the greatest mitigation effect of 3-NOP (29.6%) was observed immediately after morning feeding, and it persisted at around 23% to 26% for 10 h until the second feed provision, and 3 h thereafter, in the evening. In conclusion, supplementing 3-NOP at 60 mg/kg DM to a high-fiber diet resulted in 18% to 19% reduction in enteric CH4 emission in Swiss HF cows. The lower response to 3-NOP by BS cows was unexpected and has not been observed in other studies. These results should be interpreted with caution due to the low number of cows per breed. Finally, supplementing WCS at 5% of DM improved ECM and milk fat yield but did not enhance the CH4 inhibition effect of 3-NOP of dairy cows.

Modeling the effect of ambient temperature on reticulorumen temperature, and drinking and eating behaviors of late-lactation dairy cows during colder seasons.

Dairy cows may suffer thermal stress during the colder seasons especially due to their open-air housing systems. Free water temperature (FWT) and feed temperature (FT) are dependent on ambient temperature (AT) and can be critical for maintaining body and reticulorumen temperature (RT) in cold conditions. The objective of this study was to determine the effects of FWT and FT on RT fluctuations, and of AT on RT and drinking and eating behaviors in late-lactation cows during cold exposure. Data were collected from 16 multiparous lactating cows for four 6-d periods during the autumn and winter seasons. The cows (224 ± 36 days in milk; mean ± SD) had an average milk yield (MY) of 24.8 ± 4.97 kg/d and RT of 38.84 ± 0.163 °C. Daily average AT ranged from 4.38 to 17.25 °C. The effects of the temperature and amount of the ingested water or feed on RT change and recovery time, and the effect of the daily AT on RT, feed and water intake, and drinking, eating, and rumination behaviors were analyzed using the generalized additive mixed model framework. Reticulorumen temperature change and recovery time were affected by FWT (+0.0596 °C/°C and -1.27 min/°C, respectively), but not by FT. The amount of the ingested free water and feed affected RT change (-0.108 °C/kg drink size and -0.150 °C/kg meal size, respectively), and RT recovery time (+2.13 min/kg drink size and + 3.71 min/kg meal size, respectively). Colder AT decreased RT by 0.0151 °C/°C between 9.91 and 17.25 °C AT. Cows increased DM intake (DMI) by 0.365 kg/d per 1 °C drop in AT below 10.63 °C, but with no increase in MY. In fact, MY:DMI decreased by 0.0106/°C as AT dropped from 17.25 to 4.38 °C. Free water intake (FWI) was reduced by 0.0856 FWI:DMI/°C as AT decreased from 17.25 to 8.27 °C. Cold exposure influenced animal behavior with fewer drink and meal bouts (-0.432 and -0.290 bouts/d, respectively), larger drink sizes (+0.100 kg/bout), and shorter rumination time (-5.31 min/d) per 1 °C decrease in AT from 17.25 °C to 8.77, 12.53, 4.38, and 10.32 °C, respectively. In conclusion, exposure to low AT increased feed intake, reduced water intake, and changes in eating, drinking and rumination behaviors of dairy cows in late lactation. Additionally, the consequences of cold exposure on cows may be aggravated by ingestion of feed and free water at temperatures lower than the body, potentially impacting feed efficiency due to the extra energetic cost of thermoregulation.

Transient effect of single or repeated acute deoxynivalenol and zearalenone dietary challenge on fecal microbiota composition in female finishing pigs.

Mycotoxins are a major contaminant of pig feed and have negative effects on health and performance. The present study investigated the impact of single or repeated acute challenges with a diet naturally contaminated with deoxynivalenol (DON) and zearalenone (ZEN) on growth performances of finishing pigs and their fecal microbiota composition. A total of 160 pigs (castrated males and females) in two successive batches were randomly divided into four experimental groups of 40 pigs each. The control group received a control finisher diet from 99 to 154 days of age. Challenged groups were subjected to a 7-day acute challenge by being fed a DON- and ZEN-contaminated diet (3.02 mg DON/kg feed and 0.76 mg ZEN/kg feed) at 113 days (group DC), 134 days (group CD) or both 113 and 134 days (group DD). Microbiota composition was analyzed via 16S rRNA sequencing from fecal samples collected from the 80 females at 99, 119, 140 and 154 days. Challenged pigs (i.e. groups DC, CD and DD) reduced their average daily feed intake by 25% and 27% (P < 0.001) and feed efficiency by 34% and 28% (P < 0.05) during the first and second mycotoxin exposure, respectively. Microbiota composition was affected by mycotoxin exposure (P = 0.07 during the first exposure and P = 0.01 during the second exposure). At the family level, mycotoxin exposure significantly (P < 0.05) decreased the relative abundances of Ruminococcaceae, Streptococcaceae and Veillonellaceae and increased that of Erysipelotrichaceae at both 119 and 140 days of age. After the 7-day DON/ZEN challenge, the relative abundance of 6 to 148 operational taxonomic units (OTUs) differed among the treatment groups. However, none of these OTUs changed in all treatment groups. Using 27 functional pathways, pigs exposed to DON/ZEN challenges could be distinguished from control pigs using sparse partial least squares discriminant analysis, with a 15% misclassification rate. Regarding the functionality of these predictors, two pathways were involved in detoxifying mycotoxins: drug metabolism and xenobiotic metabolism by cytochrome P450. In challenged pigs, microbiota composition returned to the initial state within 3 weeks after the end of a single or repeated DON/ZEN challenge, highlighting the resilience of the gut microbiome. The feeding and growth performances of the pigs during challenge periods were significantly correlated with biological pathways related to health problems and modifications in host metabolism. To conclude, short-term DON/ZEN challenges resulted in transient modifications in the composition and functions of fecal microbiota.