Employee perception of precision technology use at the dairy farm.

The adoption of precision technologies on dairy farms has increased significantly in recent decades, leading to the challenge of providing employees with resources to maximize the efficient use of these tools. The objective of this study was to explore how dairy farm employees perceive the available precision technologies and to identify possible challenges they face when adapting to their use at the farm. An online survey consisting of four sections (employee demographics, precision technologies in use, perception of these technologies, and opportunities for adapting to technology use) was completed from September to December 2022 by 266 farm employees from three dairies operated under similar management. Most of the respondents were identified as male (72.2%), Hispanic or Latino (92.5%), aged between 21 and 30 (39.1%) or 31 and 40 yr (36.8%), with a bachelor's degree (34.6%) or completion of middle school (29.3%) and having basic or no English proficiency (74%). Overall, the respondents indicated being comfortable (95.6%) with and understanding (91.8%) the technology they use. Employees recognized precision technology as a tool that helps them to be more efficient (93.7%), identifying the technologies' benefits (92.1%). However, challenges for adapting to these technologies included personal limitations, such as not knowing the language of the technology (31%), visual impairments (24%), light sensitivity (14%), and not being able to read (7%). Environmental limitations were also recognized and included cold weather (64.3%), wind (46%), and surroundings that were too dark (31%) or too bright (21%). Significant associations between perception of the technology and age, level of education, and English proficiency were identified. Respondents indicated their desire to learn more about precision technologies implemented at work, which could eventually lead to improved efficiency at the dairy operation through innovations in the way users interact with these technologies, increasing employees' motivation. This study provides insights that could assist the dairy industry in addressing challenges and enhancing opportunities for a more efficient use of precision technologies at dairy farms.

Associations between early lactation intramammary infections and udder health and performance during the first 180 days in milk in first-lactation organic dairy cows.

Prior data from our group showed that first-lactation cows under organic management in United States have a high prevalence of Staphylococcus aureus, Streptococcus spp., and Staphylococcus chromogenes intramammary infections (IMI) in early lactation. Nonetheless, the relationship between IMI, udder health, and milk production in organically reared primiparous cows remains elusive. The objectives of this observational study were to investigate the relationship between presence and persistence of IMI in the first 35 d in milk (DIM) and somatic cell count (SCC) and milk production during the first 6 mo of lactation on first-lactation organic dairy cows. The analysis included a total of 1,348 composite milk samples collected during the first 35 DIM that were submitted for milk culture and 1,674 Dairy Herd Improvement Association (DHIA) tests during the first 180 DIM from 333 heifers in 4 organic dairy farms, enrolled between February 2019 and January 2020. The association between IMI in the first 35 DIM and new high SCC (SCC > 200,000 cells/mL) and milk production during the first 6 mo of lactation was investigated using Cox proportional hazards regression and mixed linear regression, respectively. The association between IMI persistence (harboring the same microorganism as reported by the laboratory for 2 or more samples) in the first 35 DIM and number of DHIA tests with high SCC during the first 6 mo of lactation was modeled using negative binomial regression. The presence of IMI by Staph. aureus (hazard ratio [HR] [95% confidence interval {CI}]: 3.35 [2.64, 4.25]) or Streptococcus spp. (HR [95% CI]: 2.25 [2.12, 2.39]) during the first 35 DIM was associated with an increased risk of new high SCC during the first 6 mo of lactation. Milk production was reduced when Streptococcus spp. were identified in milk samples. However, there was no evidence of a difference in milk production in Staph. aureus IMI. Isolation of non-aureus staphylococci and mammaliicocci was related to a mild increase in the hazards of high SCC (HR [95% CI]: 1.34 [0.97, 1.85]) and a decrease in milk production during one or more postpartum tests. Presence of gram-negative or Streptococcus-like organisms IMI was not associated with either high SCC or milk production. Presence of Bacillus IMI was associated with a lower hazard of new high SCC (HR [95% CI]: 0.45 [0.30, 0.68]), and higher milk production during the first 180 d of lactation (overall estimate [95% CI]: 1.7 kg/d [0.3, 3.0]). The persistence of IMI in the first 35 DIM was associated with the number of tests with high SCC during the lactation for all microorganisms except for Staphylococcus chromogenes. Therefore, our results suggest that the persistence of IMI in the first 35 DIM could be an important factor to understand the association between IMI detected in early lactation and lactational SCC and milk production in organic dairy heifers. Our study described associations between IMI, udder health, and milk production in first-lactation organic dairy cows that are consistent with findings from conventional dairy farms.

Associations of automated body condition scores at dry-off and through early lactation with milk yield of Holstein cows.

The objective of this study was to analyze the associations of body condition score (BCS) and BCS change (∆BCS) during the dry period and the first 100 d of lactation with daily milk yield. Examining the involvement of health status in the associations between BCS and milk yield was a secondary objective of this research. Data included 12,042 lactations in 7,626 Holstein cows calving between April 2019 and January 2022 in a commercial dairy operation located in Colorado, USA. BCSs were generated daily by an automated BCS camera system located at the exit of the milking parlor. The assessment points selected for this study were dry-off (BCSdry), calving (BCS1), 7 DIM (BCS7), 14 DIM (BCS14), 21 DIM (BCS21), and nadir (nBCS; defined as the lowest daily BCS from calving to 100 DIM). Subsequently, these BCS were categorized considering quartiles (Q1 = 25% lowest BCS; Q4 = 25% greatest BCS), separately for primiparous and multiparous cows. Changes in BCS were calculated from dry-off to calving (multiparous); and from calving to 7 DIM, 14 DIM, 21 DIM, and nadir and assigned into quartile categories considering Q1 as the 25% of cows with the greatest decrease of BCS. Lactations were classified based on the number of health events before nadir as healthy, affected by one event, or having multiple events. Data were examined in primiparous and multiparous cows separately using ANOVA. The least square means for daily milk at 60 DIM and 305 DIM were calculated by category of BCS and ∆BCS at multiple time points and time periods. Subsequently, lactation curves were created by BCS and ∆BCS categories and by health status. Multivariable models included calving season and BCS1 as covariables. The largest differences in milk yield among categories of BCS and ∆BCS were identified for BCS originated at nadir and for the ∆BCS between calving and nadir. The differences in average daily milk yield between cows in the lowest and the greatest nBCS category (Q1 vs. Q4) were 3.3 kg/d (60 DIM) and 3.4 kg/d (305 DIM) for primiparous cows and 2.4 kg/d (60 DIM) and 2.1 kg/d (305 DIM) for multiparous cows. During the period from calving to nadir, primiparous cows in Q1 (greatest decrease of BCS) produced 4.3 kg/d (60 DIM) and 3.8 kg/d (305 DIM) more than cows in Q4. For multiparous cows, the differences were 3.0 kg/d (60 DIM) and 1.9 kg/d (305 DIM) in favor of Q1 cows. Overall, the associations between BCS and ∆BCS categories and milk yield were not consistent across time and they depended on the parity category. Nonetheless, as the assessment of BCS and ∆BCS approached the nadir, the association between greater milk yield and lower BCS or greater reduction in BCS became more evident.

The objective of this study was to analyze the associations of body condition score (BCS) and BCS change (∆BCS) during the dry period and the first 100 d of lactation with daily milk yield. The involvement of health status in these associations was also evaluated. The relationship between BCS and ∆BCS with milk yield was more evident for nadir BCS (nBCS; defined as the lowest daily BCS from calving to 100 d in milk [DIM]) and for the ∆BCS occurring between calving and nBCS. Cows categorized in the lowest nBCS category and cows with greater loss in BCS from calving to nadir had the greatest average milk yields at 60 DIM and 305 DIM. In agreement, clear patterns for lactation curves were identified when the study cows were categorized by nBCS and ∆BCS for the calving to nBCS period. There was no evident association of health status with the reported relationships between BCS and milk yield.

An Evaluation of the Supplementation of Rumen-Protected Lysine and Methionine on the Lactation Performance of Fall Parturition Grazing Holstein Cows in Southern Chile.

The aim of this study was to evaluate the effect of the supplementation of rumen-protected (RP) methionine and lysine on milk yield, solids, and body weight over time on fall-calving grazing multiparous Holstein cows from Chile. Four treatment groups were studied and compared for the outcomes over time. The treatments were as follows: (i) CON: control (n = 26); (ii) RP lysine group (LYS; 20 g per cow per day; n = 26); (iii) RP methionine group (MET; 20 g per cow per day; n = 26); and (iv) LYS × MET (RP lysine and RP methionine 20 g of each amino acid per cow per day; n = 26). Data were analyzed with general linear mixed model ANOVAs for repeated measures to primarily test the main effects of each amino acid and their interactions. The supplementation of the amino acids was conducted from 2 to 70 days postpartum. Overall, milk production tended to be higher in the MET and in the LYS × MET group when compared to the control group. Furthermore, CON produced significantly less milk protein (kg) and milk fat (kg) than the LYS, MET, and LYS × MET groups. Milk urea tended to be lower during the entire study in the CON group than the rest of the groups. There was a trend for a reduction in the losses of postpartum body weight in the LYS × MET than the CON. In conclusion, RP methionine and lysine improved milk fat and protein yield in grazing multiparous cows with fall parturitions; consequently, both RP amino acids can be used as a strategy for improving grazing cows' production performance.

Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms.

Previous studies have shown that organically raised dairy cows have an increased prevalence of Staphylococcus aureus compared with conventionally raised dairy cows. However, little information exists about the dynamics of intramammary infection (IMI) in primiparous cows during early lactation on organic dairy farms. The objective of this study was to describe the IMI dynamics of primiparous cows on certified organic farms during early lactation. This longitudinal study enrolled 503 primiparous cows from 5 organic dairy farms from February 2019 to January 2020. Quarter-level milk samples were collected aseptically on a weekly basis during the first 5 wk of lactation. Samples were pooled by cow and time point into composite samples inside a sterilized laminar hood and submitted for microbiological culture. For each of the different microorganisms identified, we estimated the prevalence in each postpartum sample, period prevalence (PP), cumulative incidence, and persistence of IMI. Logistic regression models were used to investigate whether the prevalence of IMI differed by farm or sampling time points and whether IMI persistence differed between detected microorganisms. Our findings revealed a high prevalence of Staphylococcus aureus (PP = 18.9%), non-aureus staphylococci and closely related mammaliicoccal species (PP = 52.1%), and Streptococcus spp. and Streptococcus-like organisms (PP = 32.1%) within the study population. The prevalence of these microorganisms varied significantly between farms. Staphylococcus aureus and Staphylococcus chromogenes exhibited significantly higher IMI persistence compared with other detected bacterial taxa, confirming the divergent epidemiological behavior in terms of IMI chronicity across different microorganisms. This study improves our understanding of the epidemiology of mastitis-causing pathogens in organically raised primiparous cows, which can be used to tailor mastitis control plans for this unique yet growing subpopulation of dairy cows.

Impact of sensor data pre-processing strategies and selection of machine learning algorithm on the prediction of metritis events in dairy cattle.

With all the sensor data currently generated at high frequency in dairy farms, there is potential for earlier diagnosis of postpartum diseases compared with traditional monitoring methodologies. Our objectives were 1) to compare the impact of sensor data pre-processing on classifier performance by using multiple time windows before a given metritis event, while considering other cow-level factors and farm-scheduled activities; 2) to compare the performance of random forest (RF), k-nearest neighbors (k-NN), and support vector machine (SVM) classifiers at different decision thresholds using different number of past observations (time-lags) for the detection of behavioral patterns associated with changes in metritis scores; and 3) to compare classifier performance between each one of the five behaviors registered every hour by an ear-tag 3-axis accelerometer (CowManager, Agis Autimatisering, Harmelen, Netherlands). A total of 239 metritis events were created by comparing metritis scores between two consecutive clinical evaluations from cows that were retrospectively selected from a dataset containing sensor data and health information during the first 21 days postpartum from June 2014 to May 2017. Hourly sensor data classified by the accelerometer as either ruminating, eating, not active (including both standing or lying), and two different levels of activity (active and high activity) behaviors corresponding to the 3 days before each metritis event were aggregated every 24-, 12-, 6-, and 3-hour time windows. Multiple time-lags were also used to determine the optimal number of past observations needed for optimal classification. Similarly, different decision thresholds were compared in terms of model performance. Depending on the classifier, algorithm hyperparameters were optimized using grid search (RF, k-NN, SVM) and random search (RF). All behaviors changed throughout the study period and showed distinct daily patterns. From the three algorithms, RF had the highest F1 score followed by k-NN and SVM. Furthermore, sensor data aggregated every 6- or 12-h time windows had the best model performance at multiple time-lags. We concluded that the data from the first 3 days post-partum should be discarded when studying metritis, and either one of the five behaviors measured with CowManager could be used when predicting metritis when sensor data were aggregated every 6- or 12-hour time windows, and using time-lags corresponding to 2-3 days before a given event, depending on the time window used. This study shows how to maximize sensor data in their potential for disease prediction, enhancing the performance of algorithms used in machine learning.

Factors associated with the time and magnitude of the nadir body condition score in early lactation and its subsequent effects on fertility of Holstein cows.

The objective of this study was to identify variables associated with the time and magnitude of nadir BCS (nBCS) during early lactation and to characterize the effects of these two measurements on the subsequent pregnancy at first artificial insemination (P/AI1) and pregnancy loss of Holstein cows. A retrospective observational study was completed using data collected from 12,042 lactations in 7,626 Holstein cows calving between April 2019 and January 2022 in a commercial dairy operation located in Colorado, USA. Scores generated by an automated BCS camera system at dry-off (BCSdry), calving (BCS1), nadir (nBCS; defined as the lowest daily BCS from calving to 100 DIM), and 21 d post nadir were selected for the analyses and subsequently categorized into quartiles (Q1 = lower nBCS). Changes in BCS were calculated from dry-off to calving (multiparous cows); from calving to nadir; and from nadir to 21 d post nadir and assigned into quartile categories considering Q1 as the 25% of cows with greater loss (pre nadir) or smaller gain (post nadir) of BCS. Data were examined using logistic regression, ANOVA, and time to event analyses. Initial univariable models were followed by multivariable models that considered parity category, calving season, BCS1, and average milk yield up to 30 DIM (M30) as covariables. Sick cows and high producing cows had increased DIM at nadir, while lower BCSdry, greater M30, and occurrence of disease were associated with lower nBCS. Cows that conceived at AI1 had their nBCS earlier (45.1 ± 0.32 d) than cows that remained open after first AI (46.4 ± 0.35 d). On the contrary, DIM at nBCS did not differ by pregnancy loss status. The logistic regression analyses reported smaller odds of P/AI1 in cows in the lower nBCS categories. Likewise, cows with larger loss in BCS between calving and nadir had smaller odds of P/AI1. Although cows that lost their pregnancy had lower nBCS, this association was not consistent across the analyses. The time to and magnitude of nBCS, together with the ∆BCS from calving to nadir could be useful measures to evaluate the transition and early lactation status of dairy cows.

The transition from gestation to lactation requires adjustments in nutrient consumption that are challenging for the postpartum dairy cow. As milk energy output increases more rapidly than energy intake, most cows mobilize fat and labile protein from body energy reserves, which results in reductions in body condition score during early lactation. The objective of this study was to identify variables associated with the extent of the lossin body condition score (BCS) during early lactation and to characterize the effects of the nadir BCS on the subsequent pregnancy at first artificial insemination and pregnancy loss in Holstein cows. Parity, disease presentation, and milk yield were associated with the time and magnitude of nadir BCS. Sick cows and high producing cows had increased DIM at nadir, while lower BCS at dry-off, greater milk yield, and occurrence of disease were associated with lower nadir BCS. Overall, cows with later and lower nadir BCS and greater loss of BCS between calving and nadir had poorer fertility. Monitoring nadir BCS could be a useful tool for evaluating the transition and early lactation status of dairy cows.

Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins.

Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination (AI) with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein cows and produce genomic heritability estimates. Moreover, we use genomic best linear unbiased prediction (GBLUP) to investigate the potential utility of the RI by performing genomic predictions with cross validation. Notably, genomic heritability estimates for the U.S. Holstein RI were moderate (h2 = 0.1654 ± 0.0317-0.2550 ± 0.0348), while single and multi-locus GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29, including the known QTL for the daughter pregnancy rate (DPR) and cow conception rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR) QTL (59 Mb). Positional candidate genes for the detected QTL included male and female fertility loci (i.e. spermatogenesis and oogenesis), meiotic and mitotic regulators, and genes associated with immune response, milk yield, enhanced pregnancy rates, and the reproductive longevity pathway. Based on the proportion of the phenotypic variance explained (PVE), all detected QTL (n = 13; P ≤ 5e - 05) were estimated to have moderate (1.0% < PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted probability of pregnancy. Genomic prediction using GBLUP with cross validation (k = 3) produced mean predictive abilities (0.1692-0.2301) and mean genomic prediction accuracies (0.4119-0.4557) that were similar to bovine health and production traits previously investigated.

Plasma ionized calcium and magnesium concentrations and prevalence of subclinical hypocalcemia and hypomagnesemia in postpartum grazing Holstein cows from southern Chile.

The objective was to determine the plasma concentrations of ionized Ca (iCa) and Mg (iMg) and to establish the prevalence of subclinical hypocalcemia (SCHC) and hypomagnesemia (SCHM) in dairy cows at calving (within 6 hours of parturition) and at 7 days postpartum (pp) in Chilean grazing herds with spring parturitions. Plasma iCa and iMg were assessed using a clinical analyzer. A total of 113 and 175 cows in 18 herds selected at random were sampled at calving and at 7 days pp, respectively. From these 18 herds, 11 herds provided reliable records of lactation number and 8 cows per herd were scored for body condition and sampled at calving and then at 7 days pp. Ionized Ca concentrations for the 18 herds were 0.99 ± 0.16 mmol/L (calving) and 1.01 ± 0.13 mmol/L [7 d pp (P > 0.05)]. Ionized Mg concentrations were 0.58 ± 0.12 mmol/L and 0.51 ± 0.09 mmol/L (P ≤ 0.05). For the 11 herds, iCa concentrations at calving were 1.06 mmol/L (lactation 1), 1.02 mmol/L (lactation 2) and 0.89 mmol/L (lactation ≥ 3), while iMg concentrations were 0.63 mmol/L, 0.60 mmol/L, and 0.61 mmol/L, respectively. Herd prevalence for SCHC (iCa < 1.0 mmol/L) at calving was 64.8%. Prevalence by parity was 40%, 54.5% and 86.7% for lactations 1, 2 and ≥ 3, respectively. Herd prevalence of SCHC on day 7 pp was 30.1%. For SCHM (iMg < 0.52 mmol/L) prevalence was 21.6% and 48.9% at calving and at 7 days pp, respectively.

Improving the Reliability of Scale-Free Image Morphometrics in Applications with Minimally Restrained Livestock Using Projective Geometry and Unsupervised Machine Learning.

Advances in neural networks have garnered growing interest in applications of machine vision in livestock management, but simpler landmark-based approaches suitable for small, early stage exploratory studies still represent a critical stepping stone towards these more sophisticated analyses. While such approaches are well-validated for calibrated images, the practical limitations of such imaging systems restrict their applicability in working farm environments. The aim of this study was to validate novel algorithmic approaches to improving the reliability of scale-free image biometrics acquired from uncalibrated images of minimally restrained livestock. Using a database of 551 facial images acquired from 108 dairy cows, we demonstrate that, using a simple geometric projection-based approach to metric extraction, a priori knowledge may be leveraged to produce more intuitive and reliable morphometric measurements than conventional informationally complete Euclidean distance matrix analysis. Where uncontrolled variations in image annotation, camera position, and animal pose could not be fully controlled through the design of morphometrics, we further demonstrate how modern unsupervised machine learning tools may be used to leverage the systematic error structures created by such lurking variables in order to generate bias correction terms that may subsequently be used to improve the reliability of downstream statistical analyses and dimension reduction.

Liver Disorders Associated with Metabolic Imbalances in Dairy Cows.

This article discusses the complex interrelationships that originated from metabolic stress, triggering unbalances that result in suboptimal liver health. The severe changes occurring around parturition require drastic incrementation in lipolytic activity, leading to significant adipose tissue remodeling. This increased activity ultimately exceeds the liver's normal function. The inability of the liver to perform proper metabolic regulation, together with concurrent inflammatory states, altered immune status, and physiologic imbalances, results in greater risk for disease, lower milk production and fertility, and compromised well-being and lifespan in the herd.

Association between body condition score fluctuations and pregnancy loss in Holstein cows.

The objective of this study was to characterize the associations between body condition score (BCS) and BCS change (∆BCS), determined by an automated camera system during early lactation and close to artificial insemination (AI), and the subsequent pregnancy loss (PL) in Holstein cows. A secondary objective was to determine the impact of disease on PL, considering multiple time periods relative to AI. Data from 9,430 lactations in 6,884 Holstein cows in a commercial dairy operation located in Colorado, USA were included in this retrospective observational study. Cows were subject to first AI at about 80 DIM (primiparous) and 60 DIM (multiparous), following a double OvSynch protocol. Pregnancy diagnosis was performed via transrectal ultrasonography on day 32 ± 3 after AI and reconfirmed on day 80 ± 3 after AI. Cameras mounted on the sorting gate at each exit (n = 2) of the milking parlor generated BCS on a five-point scale with 0.1 increments. The BCS at calving (BCS1), 21 DIM (BCS21), 56 DIM (BCS56), AI resulting in pregnancy (BCSAI), and 90 d post AI (BCSAI90) were selected for the analyses and subsequently categorized as low (≤ lower quartile), moderate (interquartile range), and high (≥ upper quartile). Changes in BCS were calculated by periods of interest as change from calving to 21 DIM; change from calving to 56 DIM; change from 56 DIM to AI; and change from AI to 90 d post AI and assigned into categories to facilitate the analysis. Data were examined using logistic regression, considering parity category, season at calving and AI, DIM at AI, milk yield up to 60 DIM, and occurrence of disease as covariables. The logistic regression analyses indicated that the odds of PL were greater in cows in the low BCS category relative to cows in the high BCS category at 56 DIM (OR 95% CI = 1.41 [1.12-1.79]), AI (1.31 [1.05-1.65]), and 90 d post AI (1.38 [1.10-1.74]). Likewise, cows with large loss in BCS between calving and 21 DIM (1.46 [1.10-1.94]) and loss in BCS between AI and 90 d post AI (1.44 [1.15-1.81]) had greater odds of PL compared with cows with no loss of BCS within the same period. Occurrence of disease at all the time periods considered in the analysis had a consistent detrimental impact on maintenance of the pregnancy, supporting the concept that pre and postconceptional disease affects embryonic survival. Overall, low BCS, more pronounced reductions in BCS occurring closer to AI, and occurrence of disease resulted in greater PL in this Holstein population.

Maintenance of the pregnancy until term is a key factor for adequate fertility in dairy operations, as early embryonic mortality in lactating dairy cows is significant. The objective of this study was to investigate the association between the changes in body condition scores (BCS) during early lactation and in the proximity of artificial insemination (AI) and embryo mortality in Holstein cows. A secondary objective was to determine the impact of disease on pregnancy loss (PL), considering multiple time periods relative to AI. Our study population included 9,430 lactations in 6,884 Holstein cows that had their daily BCS determined by an automated camera system during early lactation and close to AI. Cows were diagnosed pregnant via transrectal ultrasonography on day 32 after AI and reconfirmed on day 80 after AI. Overall, the dynamics of BCS differed between cows that lost or did not lose their pregnancy. Low BCS and more pronounced reductions in BCS occurring closer to the AI, as well as concurrent disease, resulted in greater levels of PL.

Evaluation of Contamination in Milk Samples Pooled From Independently Collected Quarters Within a Laboratory Setting.

The primary objective of this observational study was to evaluate the prevalence of contamination from independently collected quarter-level milk samples pooled in a laboratory and subjected to bacterial culture. To address this objective, weekly quarter-level milk samples were collected longitudinally from a cohort of 503 primiparous cows from five organic dairy farms during the first 5 weeks after calving. Individual quarter milk samples were pooled in a laboratory using aseptic technique ("lab-pooled") and subjected to bacterial culture. In the sample set of 2,006 lab-pooled milk samples, 207 (10.3%) were classified as contaminated using a standard definition (i.e., growth of three or more distinct microorganisms). Subsequent culturing of corresponding quarter-level milk samples revealed that many of the contaminated lab-pooled sample results (i.e., 46.7%) were the result of intramammary infections with different pathogens across the quarters, rather than actual contamination within any single quarter (i.e., "true contamination"). The odds of true contamination were lower when the lab-pooled sample exhibited growth of three microorganisms compared to more than 3 microorganisms. Our findings suggest that pooling of quarter samples within a laboratory setting may yield lower rates of contamination compared to those previously reported from samples composited on-farm, but that current cut-offs to define contamination may need to be evaluated for use with lab-pooled samples. Further investigation of use of lab-pooled samples may be warranted to reduce costs while still providing useful scientific insight.

Effect of peripartal administration of mycobacterium cell wall fraction on health and fertility of Holstein cows under organic-certified management.

The main objective of this study was to evaluate the effect of peripartal administration of a commercially available nonspecific immune stimulant (mycobacterium cell wall fraction; MCWF [Amplimune, NovaVive Inc., Napanee, ON, Canada]) on the incidence of disease during early lactation and subsequent fertility of dairy cows. A second objective was to characterize the dynamics of circulating white blood cells (WBC) and metabolic markers following treatment administration. Cows in an United States Department of Agriculture (USDA) organic-certified dairy herd were blocked by parity and, based on sequential calving dates, randomly assigned to receive two injections (5 mL s.c.) of either a placebo (saline solution) as a control (CON; n = 71) or MCWF (n = 65) at enrollment (7 d before expected calving) and within 24 h after calving. Blood samples were collected from a subsample of the study population (MCWF = 16; CON = 18) for WBC count at enrollment, at day 2 post enrollment, and at days 1, 3, 7, and 14 after calving. Serum fatty acids, beta-hydroxybutyrate, and Ca concentrations were determined at days 1 and 7 postpartum (MCWF = 21; CON = 21). Main outcome variables included incidence risk of peripartal and early lactation health disorders and pregnancy at first artificial insemination (AI), at 100, and at 150 days in milk (DIM). In addition, the average daily milk yield up to 90 DIM and death and live culling before 305 DIM were compared. Treatment effects were assessed using multivariable logistic regression, time-to-event analyses, and repeated measures analysis of variance (ANOVA). A treatment effect on the incidence risk of some of the health disorders in the study was established. Incidence risk of metritis and clinical mastitis <28 DIM was smaller in MCWF than in CON cows (36.9% vs. 50.7% and 6.3% vs. 19.7%, respectively). On the contrary, the incidence risk of respiratory disease <28 DIM was smaller in CON (0%) than in MCWF (7.7%). Reproductive performance of multiparous cows was affected by MCWF administration: pregnancy at first AI and pregnancy at 100 and 150 DIM were greater in MCWF than in CON (35.6% vs. 19.2%; 51.1% vs. 25.0%; and 64.4% vs. 40.4%, respectively). Overall, median intervals from calving to pregnancy were 90 vs. 121 d in MCWF and CON cows, respectively. No treatment effects on the dynamics of circulating WBC or in postpartum metabolic status were established. No differences for milk yield or for the proportion of cows that survived up to 305 DIM were determined, although cows in MCWF left the herd earlier than cows in CON. In conclusion, incidence risks of metritis and mastitis in early lactation were smaller in cows receiving MCWF, whereas the incidence risk of respiratory disease was smaller in CON. Fertility significantly improved in MCWF compared with CON cows. As this study was performed in an organic-certified dairy, specific health and reproductive management practices may affect the external validity of the current findings.

Effect of oral calcium administration on metabolic status and uterine health of dairy cows with reduced postpartum rumination and eating time.

BACKGROUND: Hypocalcemia has detrimental effects on health and performance of dairy cows. As hypocalcemic cows show reduced feed intake, we hypothesized that cows with reduced combined rumination and eating time (CRET) may benefit from Ca supplementation. The objective was to evaluate the effect of postpartum oral Ca administration on metabolic status (Calcium [Ca], fatty acids [FA], and ß-Hydroxybutyrate [BHB] serum concentrations) and incidence of puerperal metritis (PM) in dairy cows with reduced postpartum CRET. Cows in an organic-certified dairy, diagnosed with reduced CRET (< 489 min/d; n = 88) during the first day postpartum were assigned into 1 of 2 treatments: i) Calcium administration (CA; n = 45) that received 1 Ca oral capsule (Bovikalc bolus, Boehringer Ingelheim, St. Joseph, MO) containing CaCl2 and CaSO4 (43 g of Ca) once per day, for 3 consecutive days, starting at d 1 postpartum; and ii) Control (CON; n = 43) that did not receive oral Ca. A convenience group consisting of cows with CRET ≥489 min/d was used for comparison and did not receive oral Ca (NOR; n = 96). RESULTS: At day 1 postpartum cows with reduced CRET had lower Ca serum concentrations (CA = 2.08 mmol/L; CON = 2.06 mmol/L) compared with NOR cows (2.17 mmol/L). Calcium concentrations at d 3, 5, and 12 postpartum were not different among the three groups. Serum FA concentrations at d 1, 3 and 5 postpartum were higher in both CA and CON cows compared with NOR. At d 12, only CA cows had higher FA concentrations than NOR cows. Serum BHB concentrations at d 3 were highest in CA, with no difference between CON and NOR. At d 5, BHB concentrations were higher in CA, followed by CON, and NOR. No effect was observed for Ca administration on incidence of PM and reproductive performance. CON cows had lower survival at 30 DIM (86.5%) than NOR cows (97.9%). CONCLUSIONS: The use of remote sensor technology identified cows with reduced rumination and eating time that had lower postpartum serum concentrations of calcium and altered metabolic status. However, oral calcium administration to cows with reduced CRET did not affect incidence of metabolic disorders nor reproductive health and subsequent pregnancy. Although survival at 30 days postpartum was lower for non-Ca supplemented cows, the identification of effective interventions in cows with reduced CRET requires further consideration.

Current attitudes of veterinarians and producers regarding the use of local and systemic analgesia in beef and dairy cattle in the United States.

OBJECTIVE: To survey cattle producers and veterinarians about the use of analgesia on US cattle operations. SAMPLE: 1,187 members of the following database, electronic mailing lists, and social media groups: FarmProgress master file, American Association of Bovine Practitioners, Academy of Veterinary Consultants, National Milk Producers Federation Farm Evaluators, Dairy Moms Facebook group, and Dairy Girl Network Facebook group. PROCEDURES: An online survey was developed to gather information about the frequency of local and systemic analgesia use for common painful procedures and diseases in cattle < 2, 2 to 12, and > 12 months old. Respondents also rated their extent of agreement with each of 10 statements related to pain management in cattle. The survey was available from June 11 to August 10, 2018. Descriptive data were generated. Logistic regression was used for comparisons among cattle age groups and respondents on the basis of their industry role. RESULTS: In general, frequency of analgesia use increased as cattle age increased, regardless of the procedure or disease. The odds of analgesia use were lower for men, compared with women, and greater for veterinarians, compared with producers. Many respondents indicated they were cognizant of the benefits of analgesia use in cattle but perceived federal regulations and drug costs as impediments to the implementation of pain mitigation protocols on cattle operations. CONCLUSIONS AND CLINICAL RELEVANCE: Results provided insight into current perceptions and use of analgesia in cattle, which can be used to guide implementation of pain mitigation protocols on US beef and dairy cattle operations.

Livestock Informatics Toolkit: A Case Study in Visually Characterizing Complex Behavioral Patterns across Multiple Sensor Platforms, Using Novel Unsupervised Machine Learning and Information Theoretic Approaches.

Large and densely sampled sensor datasets can contain a range of complex stochastic structures that are difficult to accommodate in conventional linear models. This can confound attempts to build a more complete picture of an animal's behavior by aggregating information across multiple asynchronous sensor platforms. The Livestock Informatics Toolkit (LIT) has been developed in R to better facilitate knowledge discovery of complex behavioral patterns across Precision Livestock Farming (PLF) data streams using novel unsupervised machine learning and information theoretic approaches. The utility of this analytical pipeline is demonstrated using data from a 6-month feed trial conducted on a closed herd of 185 mix-parity organic dairy cows. Insights into the tradeoffs between behaviors in time budgets acquired from ear tag accelerometer records were improved by augmenting conventional hierarchical clustering techniques with a novel simulation-based approach designed to mimic the complex error structures of sensor data. These simulations were then repurposed to compress the information in this data stream into robust empirically-determined encodings using a novel pruning algorithm. Nonparametric and semiparametric tests using mutual and pointwise information subsequently revealed complex nonlinear associations between encodings of overall time budgets and the order that cows entered the parlor to be milked.

Genomic Analysis of Visceral Fat Accumulation in Holstein Cows.

Visceral fat is related to important metabolic processes, including insulin sensitivity and lipid mobilization. The goal of this study was to identify individual genes, pathways, and molecular processes implicated in visceral fat deposition in dairy cows. Data from 172 genotyped Holstein cows classified at slaughterhouse as having low (n = 77; omental fold < 5 mm in thickness and minimum fat deposition in omentum) or high (n = 95; omental fold ≥ 20 mm in thickness and marked fat deposition in omentum) omental fat were analyzed. The identification of regions with significant additive and non-additive genetic effects was performed using a two-step mixed model-based approach. Genomic scans were followed by gene-set analyses in order to reveal the genetic mechanisms controlling abdominal obesity. The association mapping revealed four regions located on BTA19, BTA20 and BTA24 with significant additive effects. These regions harbor genes, such as SMAD7, ANKRD55, and the HOXB family, that are implicated in lipolysis and insulin tolerance. Three regions located on BTA1, BTA13, and BTA24 showed marked non-additive effects. These regions harbor genes MRAP, MIS18A, PRNP and TSHZ1, that are directly implicated in adipocyte differentiation, lipid metabolism, and insulin sensitivity. The gene-set analysis revealed functional terms related to cell arrangement, cell metabolism, cell proliferation, cell signaling, immune response, lipid metabolism, and membrane permeability, among other functions. We further evaluated the genetic link between visceral fat and two metabolic disorders, ketosis, and displaced abomasum. For this, we analyzed 28k records of incidence of metabolic disorders from 14k cows across lactations using a single-step genomic BLUP approach. Notably, the region on BTA20 significantly associated with visceral fat deposition was also associated with the incidence of displaced abomasum. Overall, our findings suggest that visceral fat deposition in dairy cows is controlled by both additive and non-additive effects. We detected at least one region with marked pleiotropic effects affecting both visceral fat accumulation and displaced abomasum.

Mind the Queue: A Case Study in Visualizing Heterogeneous Behavioral Patterns in Livestock Sensor Data Using Unsupervised Machine Learning Techniques.

Sensor technologies allow ethologists to continuously monitor the behaviors of large numbers of animals over extended periods of time. This creates new opportunities to study livestock behavior in commercial settings, but also new methodological challenges. Densely sampled behavioral data from large heterogeneous groups can contain a range of complex patterns and stochastic structures that may be difficult to visualize using conventional exploratory data analysis techniques. The goal of this research was to assess the efficacy of unsupervised machine learning tools in recovering complex behavioral patterns from such datasets to better inform subsequent statistical modeling. This methodological case study was carried out using records on milking order, or the sequence in which cows arrange themselves as they enter the milking parlor. Data was collected over a 6-month period from a closed group of 200 mixed-parity Holstein cattle on an organic dairy. Cows at the front and rear of the queue proved more consistent in their entry position than animals at the center of the queue, a systematic pattern of heterogeneity more clearly visualized using entropy estimates, a scale and distribution-free alternative to variance robust to outliers. Dimension reduction techniques were then used to visualize relationships between cows. No evidence of social cohesion was recovered, but Diffusion Map embeddings proved more adept than PCA at revealing the underlying linear geometry of this data. Median parlor entry positions from the pre- and post-pasture subperiods were highly correlated (R = 0.91), suggesting a surprising degree of temporal stationarity. Data Mechanics visualizations, however, revealed heterogeneous non-stationary among subgroups of animals in the center of the group and herd-level temporal outliers. A repeated measures model recovered inconsistent evidence of a relationships between entry position and cow attributes. Mutual conditional entropy tests, a permutation-based approach to assessing bivariate correlations robust to non-independence, confirmed a significant but non-linear association with peak milk yield, but revealed the age effect to be potentially confounded by health status. Finally, queueing records were related back to behaviors recorded via ear tag accelerometers using linear models and mutual conditional entropy tests. Both approaches recovered consistent evidence of differences in home pen behaviors across subsections of the queue.

Comparison between linseed expeller and canola expeller on concentrate intake, and circulating inflammatory mediators in Holstein calves.

The objective of this study was to compare the effect of linseed and canola expeller on average daily weight gain (ADG), concentrate intakes, incidence of diarrhea, serum haptoglobin, interleukin (IL)-1, and resolvin-E1 in female Holstein calves from birth to weaning. A sample size of 20 calves per group was calculated and were randomly allocated at the time of birth. Linseed group (LIN) was fed a starter with linseed expeller, while canola group (CAN) received a similar concentrate, but with canola expeller. Both expellers were included at a rate of 25% dry matter (DM) basis of the starter. Pasteurized waste milk was fed twice a day until weaning. Calves were weighed at birth, 30, and 60 d of age. Starter intake was evaluated daily from 5 to 60 d. A blood sample was obtained at birth, 14, 28, 35, and 49 d of age, and bovine serum resolvin-E1, haptoglobin, and IL-1 were assayed by commercial enzyme-linked immunosorbent assay (ELISA) kits. Incidence of diarrhea and the duration of the events were also recorded. The effect of the interaction group by time on body weight (BW) and starter intake was not significant (P > 0.05). Average daily gains (ADG) from 0 to 60 d for CAN and LIN groups were 0.680 and 0.675 kg/d (P > 0.05), respectively. Incidences of diarrhea were 25% and 45% for CAN and LIN groups, respectively (P = 0.18). LIN group had greater concentrations of IL-1 at d 21, haptoglobin at d 7, and resolving-E1 at d 14 and 49 than CAN group, respectively. It is concluded that BW at weaning, ADG, and concentrate intakes were not different between groups fed starters containing linseed or canola expeller (25% inclusion). The concentrations of cytokines and haptoglobin were the greatest in LIN group.