Invited review: Reproducible research from noisy data: Revisiting key statistical principles for the animal sciences

The association between somatic cell count and selective dry cow therapy, milking routine, and dry cow management practices in early-lactation cows from 21 commercial grazing dairy herds

This observational study aimed to explore the association of farmer-driven selective dry cow therapy (DCT), milking routine and dry cow management practices with SCC in early-lactation cows from 21 commercial dairy herds. Milking routine practices evaluated referred to cow preparation for milking, in-lactation mastitis management, and recording. Dry cow management practices related to dry cow environment and cleaning, dry-off procedure, milk cessation strategy and calving environment. Data from 2,016 multiparous cows in 21 commercial spring-calving grazing dairy herds were available for the study. Herd owners self-reported DCT (the assignment and administration of DCT was at the discretion of the herd owners with no involvement from the research team), management practices during milking and the dry period. Cow-level last test-day SCC records in 2020 (range = 105-285 DIM) and first test-day records in 2021 (range = 5-60 DIM) were obtained from milk recording databases. Quarter-level milk sampling was carried out on all cows in late lactation of 2020 (range = 240-261 DIM) for bacterial culturing. Bacteriological results were used to define cows with IMI when ≥1 quarter sample resulted in bacterial growth and there were no contaminated samples from that cow. Mixed model analyses were used to evaluate the association of selective DCT, milking routine, and dry cow management practices with cows' first test-day log 10 SCC (logSCC) in 2021. At dry-off in 2020, 47.6% of the cows were administered an internal teat sealant alone (ITS), while 52.4% were administered an antibiotic plus an internal teat sealant (AB+ITS). The mean herd-level percentage of cows with IMI was 19.7% (range = 9.8%-39.5%); Staphylococcus aureus accounted for the majority of cow-level IMI (89.9%, 357/397). Between herds, the proportion of cows administered ITS ranged from 17.7% (14/79; in a herd with an IMI prevalence of 10.1%) to 86.8% (66/76; in a herd with an IMI prevalence of 27.6%). In total, 11.8% (105/889) and 29.8% (292/980) of cows that were administered ITS or AB+ITS had an IMI in late lactation 2020, respectively. The mean untransformed SCC at the last test day in 2020 of cows administered ITS and AB+ITS was 55,000 and 197,200 cells/mL, respectively. The statistical analysis showed a significant interaction between selective DCT and milk yield at last test-day in 2020; cows with a milk yield of 15 kg and administered ITS had a 0.1 higher (untransformed SCC of 19,000 cells/mL higher) first test-day logSCC compared with cows administered AB+ITS. Additionally, greater parity, IMI in late lactation, higher logSCC at the last test-day in 2020 and longer dry periods were associated with higher logSCC at the first test-day in 2021. The current study identified cow- and herd-level management practices that could aid dairy farmers in improving the outcome of selective DCT and decrease early lactation SCC.

Effects of simplified group housing on behavior, welfare, growth performance, and health of preweaned dairy calves on a California dairy

Most US dairy calves are raised in individual hutches for biocontainment purposes and to facilitate monitoring and handling of calves. However, individual hutches typically restrict calves' activity and social interactions. Previous studies showed that group housing (GH) is beneficial to calf welfare and is associated with social benefits. The adoption of GH on dairies is hindered by several concerns, with the primary concern being the potential for increased transmission of diseases due to heightened calf-to-calf contact. In light of this, our study aimed to compare the behavior, health, and growth outcomes of calves housed in groups of 3 to individually housed (IH) calves during the preweaning period. A total of 42 Holstein heifer calves on a commercial dairy in Northern California were enrolled in groups of 3 to different housing treatments; IH (n = 21) or GH (n = 21) between July and October 2020. Each treatment was composed of 7 groups of 3 calves each. Calves in the GH treatment were housed in groups of 3 from 6 to 10 d until 70 d of age. Individual pens consisted of one polyethylene hutch with a 1.5 m × 1.2 m outside exercise area. Group pens were constructed by assembling 3 polyethylene hutches with a 1.5 m × 3.6 m outside exercise area of wire panel fencing. Calves were weighed and measured for height at birth and weaning. Diarrhea and bovine respiratory disease (BRD) scores were recorded daily throughout the preweaning period. Cumulative incidence and hazard ratios were estimated for BRD and diarrhea for GH and IH. A mixed model with pen as a random effect was specified to evaluate the effect of treatment. Group-housed calves gained 0.64 ± 0.02 kg/d while IH calves gained 0.65 ± 0.02 kg/d. Similarly, there was no evidence for treatment differences in withers height gain in GH calves (0.22 ± 0.01 cm/d) compared with IH calves (0.21 ± 0.01 cm/d). The cumulative incidence of BRD based on the California scoring system in GH calves was 75 ± 9.68% compared with 66.66 ± 10.28% in IH calves. Group-housed calves had a BRD hazard of 1.14 times that of IH calves (95% CI: 1.21-2.40). The cumulative incidence of diarrhea (fecal score 3) in GH calves was 100% in comparison to 95.20% ± 4.66% in IH calves. The mean proportion of scan observations of calves feeding on concentrates was significantly higher in GH (0.145 ± 0.004/h) compared with IH calves (0.076 ± 0.003/h) during the preweaning period. The study results provide evidence that this simplified GH system provides benefits of GH without detrimental short-term effects on calf growth and health during the preweaning period.

Contribution of herd management, biosecurity, and environmental factors to the risk of bovine tuberculosis in a historically low prevalence region

Eradication of bovine tuberculosis (bTB) in certain historically low-prevalence regions remains elusive. A complete characterisation of the husbandry practices, biosecurity, and environment where farms are located is crucial to implement targeted in-farm risk mitigation protocols. Here, a detailed survey performed in 94 dairy cattle farms located in Navarra, a low-prevalence region of Spain between 2016 and 2020 was carried out. Data on 73 biosecurity, farm-, and environmental-level factors potentially associated with the risk of bTB occurrence were evaluated using an ordinal logistic regression model: farms were classified based on their prevalence index, a score linked to each farm to account for the severity and recurrence of bTB cases: 22.3% of the farms had a score of 1, 21.3% a score of 2, 26.6% a score of ≥ 3, and 29.8% were negative herds. A statistically significant association between a higher prevalence index and the frequency of badger sightings along with the lease of pastures to sheep during Winter was identified. Farms that detected badgers on a monthly to daily basis in the surroundings and those that leased pastures for sheep flocks during Winter were four [odds ratio, 95% CI (4.3; 1.1-17.5)] and three (3.1; 1.0-9.9) times more likely to have the highest prevalence index, respectively (predicted probabilityprevalence index≥3 = 0.7; 95% CI 0.3-0.9). Conversely, farms that used a vehicle to transport animals from holdings to pastures were less likely (0.1; <0.1-0.3) to present higher levels of prevalence index compared with farms that used none (on foot). Results suggested that the combined effect of farm- and environmental-level risk factors identified here may be hampering disease eradication in Navarra, highlighting the need to implement targeted protocols on farms and grazing plots. An increased awareness of monitoring sheep and wildlife in direct or indirect contact with cattle herds in historically low bTB prevalence areas should be raised.

Systematic heterogenization revisited: Increasing variation in animal experiments to improve reproducibility?

Life sciences are currently facing a reproducibility crisis. Originally, the crisis was born out of single alarming failures to reproduce findings at different times and locations. Nowadays, systematic studies indicate that the prevalence of irreproducible research does in fact exceed 50%. Viewed from a rather cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. In this respect, animal research has come under particular scrutiny, as the stakes are high in terms of both research ethics and societal impact. To counteract this, it is essential to identify sources of poor reproducibility as well as to iron out these failures. We here review the current debate, briefly discuss potential reasons, and summarize steps that have already been undertaken to improve reproducibility in animal research. By the example of classical behavioural phenotyping studies, we particularly highlight the role strict standardization plays in exacerbating the crisis, and review the concept of systematic heterogenization as an alternative strategy to deal with variation in animal studies. Briefly, we argue that systematic variation rather than strict homogenization of experimental conditions benefits the robustness of research findings, and hence their reproducibility. To this end, we will present concrete examples for systematically heterogenized experiments and provide a practical guide on how to apply systematic heterogenization in experimental practice.

A randomized trial and multisite pooled trial analyses comparing effects of two hormonal implant programs and differing days-on-feed on carcass characteristics and feedlot performance of beef heifers

Research objectives were to evaluate effects of two implant programs for beef heifers fed three different durations (days-on-feed; DOF) on carcass weight and composition (primary outcomes) and feedlot performance (secondary outcomes) at commercial feedlots. Data from a randomized trial in Kansas were analyzed separately and also pooled with data from two previously published trials conducted in Texas. Heifers were randomly allocated to pens within a block, and pens were randomized to treatments in a 2 × 3 factorial randomized complete block design. Implant programs were IH + 200 - an initial Revalor-IH implant [80 mg trenbolone acetate (TBA) and 8 mg estradiol (E₂)] and a re-implant after a mean of 98-d (± 10.8 SD) with Revalor-200 (200 mg TBA and 20 mg E₂), or XH - Revalor-XH, a single extended-release implant (200 mg TBA and 20 mg E₂). Heifers were fed to a baseline endpoint (BASE; pooled mean 166-d ± 11.9 SD), +21, or +42 additional DOF. A total of 10,583 crossbred heifers with mean initial body weight (BW) 315 kg (± 20.1 SD) were enrolled in 144 pens in 24 blocks (treatment replications) across the three trials. General and generalized linear mixed models accounting for clustering of trials, blocks, and pens were used to test for effects of treatments, with significance set at α = 0.05. The only implant program × DOF interaction in pooled analyses was for dry matter intake (DMI; P < 0.01); IH + 200 heifers had lower mean DMI than XH when fed +42 DOF. Gain:feed was higher for IH + 200 compared to XH with dead and removed animals excluded (P < 0.01) or included (P = 0.03). For IH + 200, hot carcass weight (HCW) increased (P < 0.01), USDA Yield Grade (YG) distributions shifted towards lower numerical categories (P < 0.01), and Prime carcasses decreased while Select increased compared to XH (P < 0.01). For each incremental increase in DOF, final BW (P < 0.01) and HCW increased (P < 0.01), while daily gain (P < 0.01) and gain:feed (P < 0.01) decreased. Categories of YG were affected by DOF (P < 0.01); there were fewer YG 1 and 2 and more YG 4 and 5 carcasses for +42 compared to BASE and +21. USDA Quality Grade (QG) distributions differed by DOF (P < 0.01); each incremental increase in DOF resulted in more Prime and fewer Select carcasses. Without meaningful interactions, tested implant programs likely have a consistent effect when heifers are fed to similar DOF, while changes in HCW, QG, and YG may influence marketing decisions when extending DOF.

Caught on Camera: On the Need of Responsible Use of Video Observation for Animal Behavior and Welfare Research

Video analysis is a popular and frequently used tool in animal behavior and welfare research. In addition to the actual object of research, video recordings often provide unforeseen information about the progress of the study, the animals or the people involved. Conflicts can arise when this information is weighed against the original intention of the recordings and broader social expectations. Uncertainty may prevent the video observers, often less experienced researchers, to properly address these conflicts, which can pose a threat to animal welfare and research quality and integrity. In this article, we aim to raise awareness of the interrelationship of variables characteristic for video-based animal studies and the potential conflicts emerging from this. We propose stepping stones for a framework which enables a culture of openness in dealing with unexpected and unintended events observed during video analysis. As a basis, a frame of reference regarding privacy and duty of care toward animals should be created and shared with all persons involved. At this stage, expectations and responsibilities need to be made explicit. During running and reporting of the study, the risk of animal welfare and research integrity issues can be mitigated by making conflicts discussible and offering realistic opportunities on how to deal with them. A practice which is outlined and guided by conversation will prevent a mere compliance-based approach centered on checklists and decision trees. Based on these stepping stones, educational material can be produced to foster reflection, co-creation and application of ethical practice.

A reply to "Relevant factors in the eutrophication of the Uruguay River and the Río Negro"

A recent paper by Beretta-Blanco and Carrasco-Letelier (2021) claims that agricultural eutrophication is not one of the main causes for cyanobacterial blooms in rivers and artificial reservoirs. By combining rivers of markedly different hydrological characteristics e.g., presence/absence and number of dams, river discharge and geological setting, the study speculates about the role of nutrients for modulating phytoplankton chlorophyll-a. Here, we identified serious flaws, from erratic and inaccurate data manipulation. The study did not define how erroneous original dataset values were treated, how the variables below the detection/quantification limit were numerically introduced, lack of mandatory variables for river studies such as flow and rainfall, arbitrary removal of pH > 7.5 values (which were not outliers), and finally how extreme values of other environmental variables were included. In addition, we identified conceptual and procedural mistakes such as biased construction/evaluation of model prediction capability. The study trained the model using pooled data from a short restricted lotic section of the (large) Uruguay River and from both lotic and reservoir domains of the Negro River, but then tested predictability within the (small) Cuareim River. Besides these methodological considerations, the article shows misinterpretations of the statistical correlation of cause and effect neglecting basic limnological knowledge of the ecology of harmful algal blooms (HABs) and international research on land use effects on freshwater quality. The argument that pH is a predictor variable for HABs neglects overwhelming basic paradigms of carbon fluxes and change in pH because of primary productivity. As a result, the article introduces the notion that HABs formation are not related to agricultural land use and water residence time and generate a great risk for the management of surface waterbodies. This reply also emphasizes the need for good practices of open data management, especially for public databases in view of external reproducibility.

A multi-herd study shows that saliva is more than a reflection of serum biomarkers in pigs

This study evaluates if biomarkers of porcine health status in saliva samples is a mere reflection of serum to detect disease in pigs under field conditions. Four farms from the same commercial company were included to obtain samples from animals with different pathological conditions. A total of 10 healthy animals and 10-15 animals from each farm with clinical symptoms of the disease were sampled for paired saliva and blood during a veterinary clinical visit. The biomarker panel included acute-phase proteins (APPs), C-reactive protein (CRP), haptoglobin (Hp), an inflammatory marker, adenosine deaminase (ADA), the total antioxidant capacity (TAC), the levels of essential trace elements, copper (Cu) and zinc (Zn), and the measurement of the total protein content (TP). After detailed statistical analysis, the results showed that saliva could replace serum for APP measurements since a good agreement has been observed between the concentrations of APPs in both body fluids. For any other biomarker, no agreement between the concentrations quantified in serum and saliva samples was observed visually. However, salivary ADA and TP concentrations were statistically significantly higher in the diseased, whereas the statistical tests with serum concentrations were inconclusive. Furthermore, greater differentiation between healthy and diseased animals could be observed when the distribution of biomarkers was analysed in saliva than in other serum samples. The diagnostic power to discriminate between healthy and diseased pigs is similar in saliva and in serum samples. Preliminary regression models may offer an optimal combination of biomarkers for disease detection in saliva (Hp, CRP, and TAC) and serum (Hp, CRP, and Cu), which demands less labour, sample, and financial cost for saliva determinations. The contradictory results observed for TAC, Cu, and Zn levels between body fluids indicate a need for further studies. To sum up, saliva-based biomarkers instead of serum-based biomarkers could contribute to more efficient detection of diseased animals.

One Coin, Two Sides: Eliciting Expert Knowledge From Training Participants in a Capacity-Building Program for Veterinary Professionals

Scientific research may include the elicitation of judgment from non-academic subject-matter experts in order to improve the quality and/or impact of research studies. Elicitation of expert knowledge or judgment is used when data are missing, incomplete, or not representative for the specific setting and processes being studied. Rigorous methods are crucial to ensure robust study results, and yet the quality of the elicitation can be affected by a number of practical constraints, including the understanding that subject-matter experts have of the elicitation process itself. In this paper, we present a case of expert elicitation embedded within an extended training course for veterinary professionals as an example of overcoming these constraints. The coupling of the two activities enabled extended opportunities for training and a relationship of mutual respect to be the foundation for the elicitation process. In addition, the participatory research activities reinforced knowledge synthesis objectives of the educational program. Finally, the synergy between the two concurrent objectives may produce benefits which transcend either independent activity: solutions and ideas built by local professionals, evolving collaborative research and training approaches, and a network of diverse academic and practicing professionals. This approach has the versatility to be adapted to many training and research opportunities.

Incorporating inter-individual variability in experimental design improves the quality of results of animal experiments

Inter-individual variability in quantitative traits is believed to potentially inflate the quality of results in animal experimentation. Yet, to our knowledge this effect has not been empirically tested. Here we test whether inter-individual variability in emotional response within mouse inbred strains affects the outcome of a pharmacological experiment. Three mouse inbred strains (BALB/c, C57BL/6 and 129S2) were behaviorally characterized through repeated exposure to a mild aversive stimulus (modified Hole Board, five consecutive trials). A multivariate clustering procedure yielded two multidimensional response types which were displayed by individuals of all three strains. We show that systematic incorporation of these individual response types in the design of a pharmacological experiment produces different results from an experimental pool in which this variation was not accounted for. To our knowledge, this is the first study that empirically confirms that inter-individual variability affects the interpretation of behavioral phenotypes and may obscure experimental results in a pharmacological experiment.

Inter-individual variability in habituation of anxiety-related responses within three mouse inbred strains

Inter-individual variability in behavioral and physiological response has become a well-established phenomenon in animal models of anxiety and other disorders. Such variability is even demonstrated within mouse inbred strains. A recent study showed that adaptive and non-adaptive anxiety phenotypes (measured as habituation and/or sensitization of anxiety responses) may differ within cohorts of 129 mice. This variability was expressed across both anxiety- and activity-related behavioral dimensions. These findings were based however on re-analysis of previously published data. The present study therefore aimed to empirically validate these findings in 129 mice. In addition, we assessed such inter-individuality in two other strains: BALB/c and C57BL/6. Males of three mouse inbred strains (BALB/c, C57BL/6 and 129S2) were behaviorally characterized through repeated exposure to a mild aversive stimulus (modified Hole Board, 4 consecutive trials). Behavioral observations were supplemented with assessment of circulating corticosterone levels. Clustering the individual response trajectories of behavioral and endocrine responses yielded two multidimensional response types of different adaptive value. Interestingly, these response types were displayed by individuals of all three strains. The response types differed significantly on anxiety and activity related behavioral dimensions but not on corticosterone concentrations. This study empirically confirms that adaptive capacities may differ within 129 cohorts. In addition, it extends this inter-individual variability in behavioral profiles to BALB/c and C57BL/6. Whether these two sub-types constitute differential anxiety phenotypes may differ per strain and requires further study.

Effects of rumen-protected choline supplementation in Holstein dairy cows during electric heat blanket-induced heat stress

Dairy cows experiencing heat stress (HS) attempt to thermoregulate through multiple mechanisms, such as reducing feed intake and milk production and altering blood flow to increase heat dissipation. Effects of choline on energy metabolism and immune function may yield it a viable nutritional intervention to mitigate negative effects of HS. The primary objective of this experiment was to determine if supplementation of rumen-protected choline during, or before and during, an increased heat load would ameliorate the negative effects of HS on production and immune status. Heat stress was induced via an electric heat blanket model with a 3-d baseline period and 7-d HS period for all cows. Multiparous mid-lactation (208 ± 31 days in milk) Holstein cows were fed the same basal herd diet, blocked by pre-experiment milk yield, and randomly assigned to receive one of the following: (1) no rumen-protected (RP) choline (n = 7); (2) RP choline (60 g/d) via top-dress during the HS period (n = 8); or (3) RP choline (60 g/d) via top-dress during the baseline and HS periods (n = 8). Imposing HS via electric heat blanket raised respiration rate with all cows surpassing the HS threshold of 60 breaths/min. The increase in respiration rate tended to be ameliorated with either schedule of RP choline supplementation. Milk yield tended to increase when RP choline was supplemented in both the baseline period and during HS. Supplementation of RP choline tended to reduce blood fatty acid and triglyceride and tended to increase the revised quantitative insulin sensitivity check index. The role of RP choline supplementation to partially ameliorate the effects of HS should be further explored as a potential nutritional strategy to mitigate the negative consequences of HS on health and production.

Controlled trial of the effect of negative dietary cation-anion difference prepartum diets on milk production, reproductive performance, and culling of dairy cows

Our objective was to assess the effects of feeding negative dietary cation-anion difference (DCAD) prepartum diets on milk production, reproductive performance, and culling. Cows from 4 commercial farms in Ontario, Canada were enrolled in a pen-level controlled trial from November 2017 to April 2019. Close-up pens (1 per farm) with cows 3 wk before calving were randomly assigned to a negative DCAD (TRT; -108 mEq/kg of dry matter; target urine pH 6.0-6.5) or a control diet (CON; +105 mEq/kg of dry matter with a placebo supplement). Each pen was fed TRT or CON for 3 mo (1 period), and then switched to the other treatment for the next period (4 periods per farm). Data from 15 experimental units (8 pen treatments in TRT and 7 in CON), with a total of 1,086 observational units (cows), were included. The effect of treatment on milk yield at the first 3 milk recording tests of lactation was assessed with linear regression models accounting for repeated measures. The risk of pregnancy at first artificial insemination and culling by 30, 60, and 305 d in milk (DIM) were analyzed with logistic regression models, and effects on time to first AI, pregnancy, and culling were assessed with Cox proportional hazards models. All models included treatment, parity, and their interactions, accounting for pen-level randomization and clustering of animals within farm with random effects, giving 10 degrees of freedom for treatment effects. Multiparous cows fed TRT produced more milk at the first (42.0 vs. 38.8 ± 1.2 kg/d) and second (44.2 vs. 41.7 ± 1.3 kg/d) milk tests. However, multiparous cows fed TRT tended to have 0.2 percentage units less milk fat content at these tests. Although multiparous cows fed TRT tended to have greater energy-corrected milk at the first test (least squares means ± standard error: TRT = 46.1 ± 0.9 vs. CON = 43.8 ± 1 kg/d), there were no differences observed in energy-corrected milk at the second or third tests. In primiparous cows, there was no effect of treatment on milk production. Multiparous cows fed TRT had greater pregnancy to first insemination (TRT = 42 ± 3 vs. CON = 32 ± 4%) and tended to have shorter time to pregnancy [hazard ratio (HR) = 1.20; 95% CI: 0.96-1.49]. In primiparous cows fed TRT, time to pregnancy was increased (HR = 0.76; 95% CI: 0.59-0.99). Culling by 30 DIM tended to be less in TRT (3.3 ± 1.1%) than CON (5.5 ± 1.8%). No effect of treatment on culling by 305 DIM was detected in primiparous cows, but in multiparous cows, the TRT diets decreased the odds of culling (21.3 ± 1.9 vs. 31.7 ± 2.8%) and daily risk of culling to 305 DIM (HR = 0.64; 95% CI: 0.46 to 0.89). Under commercial herd conditions, prepartum negative DCAD diets improved milk production and reproductive performance, and reduced culling risk in multiparous cows. In primiparous cows, TRT diets had no effect on milk yield or culling, but increased the time to pregnancy. Our results suggest that negative DCAD diets should be targeted to multiparous cows.

Controlled trial of the effect of negative dietary cation-anion difference on postpartum health of dairy cows

The objective of this study was to assess the effects of feeding negative dietary cation-anion difference (DCAD) dry cow diets on postpartum health. Cows from 4 commercial dairy farms in Ontario, Canada, were enrolled in a pen-level controlled trial from November 2017 to April 2019. Close-up pens (1 per farm), with cows 3 wk before expected calving, were randomly assigned to a negative DCAD [TRT; -108 mEq/kg of dry matter (DM); target urine pH 6.0-6.5] or a control diet (CON; +105 mEq/kg of DM with a placebo supplement). Each pen was fed TRT or CON for 3 mo (1 period) then switched to the other treatment for the next period, with 4 periods per farm. Urine pH was measured weekly until calving, and body condition score (BCS) was measured at enrollment and at 5 wk postpartum. Data from 15 experimental units [8 TRT and 7 CON, with 1,086 (TRT: n = 681; CON: n = 405) observational units (cows)] that received the assigned diet for >1 wk were included. The incidence of milk fever (MF), retained placenta (RP), metritis, hyperketonemia (blood β-hydroxybutyrate >1.2 mmol/L, measured weekly in wk 1 and 2), clinical mastitis within 30 DIM (MAST), displaced abomasum (DA) within 30 d in milk (DIM), purulent vaginal discharge (PVD, assessed once at wk 5), and number of disease events (≥1 or ≥2) were analyzed with logistic regression models with treatment, parity, BCS, and their interactions, accounting for pen-level randomization and clustering of animals within farm with random effects, giving 10 degrees of freedom to test treatment effects. Multiparous cows fed TRT had greater blood calcium between 1 and 4 DIM than multiparous cows fed CON, and the prevalence of subclinical hypocalcemia (total Ca ≤2.14 mmol/L) was lesser when fed TRT compared with CON (d 1: 73 ± 6% vs. 93 ± 4%; d 2: 65 ± 7% vs. 90 ± 5%), with no differences between treatments detected in primiparous cows. We detected interactions of treatment and BCS at enrollment for MF in multiparous cows and of treatment and parity for ≥2 disease events. Overconditioned (BCS ≥3.75) multiparous cows had reduced incidence of MF when fed TRT (TRT: 2 ± 1%, vs. CON: 13 ± 8%). We detected no treatment effects on RP, metritis, hyperketonemia, or PVD incidence. Cows fed TRT had lesser incidence of DA (1.7 ± 0.7% vs. 3.6 ± 1.6%) and tended to have lesser incidence of MAST compared with CON (1.8% ± 0.6% vs. 4.4 ± 1.4%). No treatment effect was detected on ≥1 disease events (TRT: 38 ± 7%, vs. CON: 42 ± 8%); however, multiparous cows on TRT were less likely to have ≥2 disease events than cows on CON (14 ± 4% vs. 23 ± 6%). Under commercial herd conditions, feeding prepartum diets with negative DCAD improved several measures of postpartum health.

3-Nitrooxypropanol Decreased Enteric Methane Production From Growing Beef Cattle in a Commercial Feedlot: Implications for Sustainable Beef Cattle Production

Effects of the investigational methane (CH4) inhibitor 3-nitrooxypropanol (3-NOP) on animal performance, health and enteric CH4 production of beef cattle were evaluated in a commercial feedlot. Two concurrent studies were conducted: a large pen study (4,048 cattle, eight pen replicates per experimental group) to measure animal performance and health and a small pen study (a subset of 50 cattle from the large pen study, n = 25 per experimental group) to measure enteric CH4 emissions. Within the study, animals (body weight ± SD, 282 ± 8 kg) were assigned in a completely randomized design to one of two groups: control, fed a backgrounding diet (70% corn or barley silage, 30% steam-flaked barley grain concentrate; dry matter (DM) basis) and 3-NOP, fed the backgrounding diet containing 3-NOP. The treatment group in the large pen study was adapted to 3-NOP (12 ± 3 d) before receiving the final target level of 200 mg/kg of DM, which was fed for 108 ± 8 d. Animals in the small pen CH4 emissions study received a basal diet or a basal diet with 3-NOP, with the dose increased every 28 d: low (150 mg/kg DM; 1.27 g/d), medium (175 mg/kg DM; 2.25 g/d), and high (200 mg/kg DM; 2.75 g/d). Intake in the small pens was monitored by electronic feeding bunks and CH4 was measured using the GreenFeed system. In the large pen study, total weight gained, average daily gain, and animal health variables were not affected by 3-NOP, but DM intake (DMI) tended to decrease (P = 0.06) by 2.6% relative to control (8.07 kg/d), while gain:feed ratio tended to be improved (P = 0.06) by 2.5% relative to control (0.161 kg weight gain/kg DMI). In the small pen study, average daily consumption of 3-NOP increased with inclusion rate whereas average DMI was decreased by 5.4% (P = 0.02) compared with control (10.4 kg/d). On average, addition of 3-NOP decreased (P = 0.001) CH4 emissions (g/d) by 25.7% and yield (g CH4/kg DMI) by 21.7%. In conclusion, supplementing a backgrounding diet with 3-NOP decreased CH4 yield and tended to improve feed efficiency of beef cattle fed in a commercial feedlot with no negative impacts on animal health.

Greater liver PNPLA3 protein abundance in vivo and in vitro supports lower triglyceride accumulation in dairy cows

Fatty liver syndrome is a prevalent metabolic disorder in peripartum dairy cows that unfavorably impacts lactation performance and health. Patatin-like phospholipase domain-containing protein 3 (PNPLA3) is a lipase that plays a central role in human non-alcoholic fatty liver disease etiology but has received limited attention in bovine fatty liver research. Thus, we investigated the relationship between tissue PNPLA3 expression and liver triglyceride accumulation in vivo via a ketosis induction protocol in multiparous dairy cows peripartum, as well as in vitro via small interfering RNA knockdown of PNPLA3 mRNA expression in bovine primary hepatocytes. Results demonstrated a negative association (P = 0.04) between liver PNPLA3 protein abundance and liver triglyceride content in peripartum dairy cows, while adipose PNPLA3 protein abundance was not associated with liver triglyceride content or blood fatty acid concentration. Knockdown of PNPLA3 mRNA resulted in reduced PNPLA3 protein abundance (P < 0.01) and greater liver triglyceride content (P < 0.01). Together, these results suggest greater liver PNPLA3 protein abundance may directly limit liver triglyceride accumulation peripartum, potentially preventing bovine fatty liver or accelerating recovery from fatty liver syndrome.

Risk factors for bovine periodontal disease - a preliminary study

The work presented in this pilot study aimed to identify potential risk factors associated with bovine periodontitis development. Bovine periodontitis is a multifactorial polymicrobial infectious disease for which the aetiopathogenesis and risk factors are not fully understood. From cattle slaughtered in an abattoir in Scotland, 35 dental arcades with periodontal lesions and 40 periodontally healthy arcades were selected over seven visits for study. Multivariable logistic regression analysis was used to evaluate the association between periodontitis and the independent variables, gender, age and breed. For every increase in year of age, cattle were 1.5 times more likely to have periodontitis. A graphical analysis indicated that within the limits of this study, we could not detect any major influence of breed on the age-effect. Although logistic regression analysis demonstrated that periodontitis lesions are more prevalent with increasing age of cattle the underlying mechanisms remain unclear. It is likely that periodontitis is an important cause of oral pain in older cattle and can contribute to reduced productivity/performance. Further studies with a larger sample size are necessary to elucidate the associations between potential risk factors and periodontitis in cattle and to define its effects on animal welfare and productivity.

An individual based, multidimensional approach to identify emotional reactivity profiles in inbred mice

BACKGROUND

Despite extensive environmental standardization and the use of genetically and microbiologically defined mice of similar age and sex, individuals of the same mouse inbred strain commonly differ in quantitative traits. This is a major issue as it affects the quality of experimental results. Standard analysis practices summarize numerical data by means and associated measures of dispersion, while individual values are ignored. Perhaps taking individual values into account in statistical analysis may improve the quality of results.

NEW METHOD

The present study re-inspected existing data on emotional reactivity profiles in 125 BALB/cJ and 129 mice, which displayed contrasting patterns of habituation and sensitization when repeatedly exposed to a novel environment (modified Hole Board). Behaviors were re-analyzed on an individual level, using a multivariate approach, in order to explore whether this yielded new information regarding subtypes of response, and their expression between and within strains.

RESULTS

Clustering individual mice across multiple behavioral dimensions identified two response profiles: a habituation and a sensitization cluster.

COMPARISON WITH EXISTING METHOD(S)

These retrospect analyses identified habituation and sensitization profiles that were similar to those observed in the original data but also yielded new information such as a more pronounced sensitization response. Also, it allowed for the identification of individuals that deviated from the predominant response profile within a strain.

CONCLUSIONS

The present approach allows for the behavioral characterization of experimental animals on an individual level and as such provides a valuable contribution to existing approaches that take individual variation into account in statistical analysis.

Postpartum supplementation with fermented ammoniated condensed whey altered nutrient partitioning to support hepatic metabolism

Our previously published paper demonstrated that fermented ammoniated condensed whey (FACW) supplementation improved feed efficiency and metabolic profile in postpartum dairy cows. The objective of this study was to further explore the effects of FACW supplementation on liver triglyceride content, hepatic gene expression and protein abundance, and plasma biomarkers related to liver function, inflammation, and damage. Individually fed multiparous Holstein cows were blocked by calving date and randomly assigned to postpartum (1 to 45 d in milk, DIM) isonitrogenous treatments: control diet (n = 20) or diet supplemented with FACW (2.9% dry matter of diet as GlucoBoost; Fermented Nutrition, Luxemburg, WI, replacing soybean meal; n = 19). Liver biopsies were performed at 14 and 28 DIM for analysis of mRNA expression, protein abundance, and liver triglyceride content. There was marginal evidence for a reduction in liver triglyceride content at 14 DIM in FACW-supplemented cows compared with the control group. Cows supplemented with FACW had greater mRNA expression of glucose-6-phosphatase at 14 DIM relative to control. Supplementation with FACW increased mRNA expression of pyruvate carboxylase (PC), but did not alter cytosolic phosphoenolpyruvate carboxykinase (PCK1), resulting in a 2.4-fold greater PC:PCK1 ratio for FACW-supplemented cows compared with control. There was no evidence for a FACW effect on mRNA expression of propionyl-CoA carboxylase nor on mRNA expression or protein abundance of lactate dehydrogenase A or B. Cows supplemented with FACW had lower plasma urea nitrogen compared with control. Plasma l-lactate was greater for FACW-supplemented cows compared with control at 2 h before feeding time at 21 DIM. There was no evidence for altered expression of IL1B or IL10, or blood biomarkers related to liver function and damage. Greater glucose-6-phosphatase and PC gene expression, together with greater blood glucose and similar milk lactose output, suggests that FACW increased the supply of glucose precursors, resulting in greater gluconeogenesis between 3 and 14 DIM. Greater hepatic PC:PCK1 ratio, together with previously reported decreased plasma β-hydroxybutyrate and the marginal evidence for lower liver triglyceride content at 14 DIM, suggests greater hepatic capacity for complete oxidation of fatty acids in FACW-supplemented cows compared with control. Overall, improvements in metabolite profile and feed efficiency observed with postpartum supplementation of FACW may be attributed to increased gluconeogenic and anaplerotic precursors, most likely propionate, due to modulated rumen fermentation.

The effect of prepartum negative dietary cation-anion difference and serum calcium concentration on blood neutrophil function in the transition period of healthy dairy cows

Our objectives were to assess the effects of a diet with a negative dietary cation-anion difference (DCAD) before calving on phagocytosis (Pc) and oxidative burst (OB) function of circulating neutrophils, and to determine the associations of serum ionized (iCa) and total calcium (tCa) concentrations with Pc and OB in transition dairy cows. We hypothesized that multiparous cows fed a negative DCAD diet prepartum would have greater iCa and tCa, and thus improved Pc and OB. From 3 wk before expected parturition until calving, 38 healthy multiparous cows from 3 farms were assigned to negative DCAD treatment (TRT; -100 mEq/kg of diet dry matter; n = 21) or a control (CON; 95 mEq/kg of dry matter; n = 17) diet. Each farm was on one treatment or the other at a time, but all farms contributed cows to both groups. Urine pH was measured weekly and in TRT was 6.1 ± 0.8 with 80% of 50 samples <7 and 74% ≤ 6.5. Phagocytosis, OB, iCa, and tCa were measured at d -7, 1, and 4 relative to calving. Median fluorescence intensity for Pc (MFIP) and OB (MFIOB), and the shift of percentage of cells active for Pc (PPc) and OB (POB) were measured in isolated, stimulated neutrophils via flow cytometry. Outcomes were assessed with mixed linear regression models accounting for repeated measures. There were no differences between treatments in the 4 neutrophil function outcomes. Although MFIOB varied over time, there were no interactions of treatment with time for any outcome. Serum ionized and tCa did not differ between TRT and CON. The least squares means ± standard deviation for iCa were: d -7, 1.23 ± 0.12 vs. 1.21 ± 0.12; d 1, 1.07 ± 0.12 vs. 1.02 ± 0.12; d 4, 1.16 ± 0.12 vs. 1.17 ± 0.12 mmol/L for TRT and CON, respectively; and for tCa: d -7 2.39 ± 0.25 vs 2.44 ± 0.31; d 1, 2.01 ± 0.25 vs 1.97 ± 0.31; d 4, 2.33 ± 0.25 vs 2.32 ± 0.31 mmol/L, respectively. The proportion of blood samples with tCa <2.15mmol/L at d -7, 1 and 4 was 5, 76, and 13%, respectively, with no differences between TRT and CON. Correlations of iCa or tCa with each of the 4 polymorphonuclear leukocyte (PMN) function outcomes were weak (r < |0.3|). We did not observe the hypothesized differences in aspects of innate immunity in clinically healthy multiparous cows fed a negative DCAD. We underline that cows that experienced clinical disease were excluded from this study, which is important for interpretation of the results.

High biosecurity and welfare standards in fattening pig farms are associated with reduced antimicrobial use

In order to reduce antimicrobial use in pig production, the consequences of insufficient biosecurity and welfare problems need to be known. This study aimed to investigate associations between the number of antimicrobial treatments per fattening pig, and biosecurity, indicators for animal welfare as well as the prevalence of lesions at slaughter. The data used in this study were extracted from the pig health and welfare classification system (Sikava), which gathers data on medicine usage, meat inspection, animal welfare and the condition of farm buildings from over 95% of pig production in Finland. The data were registered during years from 2011 to 2013. Upon antimicrobial prescription, information on the number of fattening pigs treated and the main reason for treatment was recorded. In addition, at least 4 times per year, pig farms registered in Sikava were visited by the farm veterinarian who assessed, among other things, biosecurity and indicators for animal welfare (air quality, condition of facilities, cleanliness, enrichment and stocking density). Finally, data from slaughterhouse inspections were collected (number of carcasses with joint infection, abscesses, lung lesions, pleurisy and liver lesions). For analysis, these datasets were aggregated at the farm level to a quarter of a year. During the studied period, the mean number of antimicrobial treatments per fattening pig per 3 months was equal to 0.09. The main reasons for antimicrobial treatments were musculoskeletal diseases, tail biting and respiratory disorders (42, 33 and 12% of diagnoses, respectively). The meat inspection scoring indicated that as much as 14.7% of all pigs had pleurisy, 5.3% liver lesions and 4.1% abscesses. A standard zero-inflated negative binomial model was used to identify factors associated with the number of antimicrobial treatments per pig. The count of antimicrobial treatments per pig increased with the size of a farm. Regardless of prevalence of lesions, farms with poor drinking equipment, insufficient enrichment and a combination of poor condition of pens and high stocking density were associated with an increased number of antimicrobial treatments for musculoskeletal diseases per pig. Problems with stocking density and enrichment were associated with the number of antimicrobial treatments for tail biting, although these results depended on prevalence of joint infections. Problems with air quality and the combination of poor cleanliness and poor condition of facilities were associated with increased number of antimicrobial treatments due to respiratory diseases. This study suggests that by improving biosecurity and welfare at pig farms, antimicrobial use can be reduced.

Bacterial concentrations in bedding and their association with dairy cow hygiene and milk quality

Comparison of bacterial counts (BCs) among common bedding types used for dairy cows, including straw, is needed. There is concern that the microbial content of organic bedding is elevated and presents risks for dairy cow udder health and milk quality. The objectives of this study were to investigate: (1) % DM and BCs (Streptococcus spp., all gram-negatives and specifically Klebsiella spp.) in different types of bedding sampled, and to investigate housing and farm management factors associated with % DM and BCs; (2) if bedding type was associated with hygiene of cow body parts (lower-legs, udder, upper-legs and flank) and housing and management factors associated with hygiene and (3) bedding types associated with higher BCs in cow milk at the farm level and bulk tank milk and management factors that were associated with highest BCs. Seventy farms (44 free-stall and 26 tie-stall) in Ontario, Canada were visited 3 times, 7 days apart from October 2014 to February 2015. At each visit, composite samples of unused and used bedding were collected for % DM determination and bacterial culture. Used bedding samples were collected from the back third of selected stalls. Data were analyzed using multivariable linear mixed models. Bedding classification for each farm were: new sand (n = 12), straw and other dry forage (n = 33), wood products (shavings, sawdust; n = 17) and recycled manure solids (RMSs)-compost, digestate (n = 8). In used bedding, across all bedding samples, sand was driest, compared to straw and wood, and RMS; higher % DM was associated with lower Streptococcus spp. count. Streptococcus spp. and all Gram-negative bacteria counts increased with increasing days since additional bedding was added. Gram-negative bacteria counts in used bedding varied with type: RMS = 16.3 ln colony-forming units (cfu)/mL, straw = 13.8 ln cfu/mL, new sand = 13.5 ln cfu/mL, and wood = 10.3 ln cfu/mL. Klebsiella spp. counts in used bedding were lower for wood products (5.9 ln cfu/mL) compared to all other bedding types. Mean cow SCC tended to be higher on farms with narrower stalls. Farms with mattress-based stalls had a higher prevalence of cows with dirty udders compared to those using a deep bedding system (often inorganic sand). Wider stalls were associated with lower bulk milk bacteria count. Lower % DM of used bedding was associated with higher bulk milk bacteria count. In conclusion, bedding management may have a profound impact on milk quality, bacterial concentrations in the bedding substrates, and cow hygiene.

Refining animal research: The Animal Study Registry

The Animal Study Registry (ASR; www.animalstudyregistry.org) was launched in January 2019 for preregistration of animal studies in order to increase transparency and reproducibility of bioscience research and to promote animal welfare. The registry is free of charge and is designed for exploratory and confirmatory studies within applied science as well as basic and preclinical research. The registration form helps scientists plan their study thoroughly by asking detailed questions concerning study design, methods, and statistics. With registration, the study automatically receives a digital object identifier (DOI) that marks it as intellectual property of the researcher. To accommodate the researchers concerns about theft of ideas, users can restrict the visibility of their registered studies for up to 5 years. The full content of the study becomes publicly accessible at the end of the embargo period. Because the platform is embedded in the infrastructure of the German Federal Government, continuity and data security are provided. By registering a study in the ASR, researchers can show their commitment to transparency and data quality to reviewers and editors, to third-party donors, and to the general public.

Comparison of effects of four weaning methods on health and performance of beef calves

Weaning of beef calves is a stressful event that negatively impacts health and performance. A variety of interventions have been proposed to reduce stress and improve gains following weaning. This study used 288 7- to 8-month-old calves from two separate locations, to examine four different weaning strategies, as well as the impact of shipment. Calves were blocked by weight and sex, and then randomly assigned to one of four treatments: abrupt weaning (AW), where calves were separated from the dam on day 0 (D0) and allowed no further contact with the dam; fence line (FL), where calves were weaned on D0 but had fence line contact with dams for 7 days; nose flap (NF), where on day -6 calves received a nose flap that interferes with suckling, then had the flap removed and were weaned from the dam on D0; and intermittent separation (SEP), where calves were removed from dams for 24-h intervals on day -13 and day -6, then weaned on D0, but allowed fence line contact with the dam for 7 days. Each treatment group was further divided into two subgroups, one of which was shipped early (D0 for AW, day 7 for others) or shipped later (day 28). Body weight and sickness were recorded for all groups. Results showed a negative impact on gain for early shipping compared to later shipping, and poorer gain in AW calves than most other treatments. Results of the analyses of morbidity were inconclusive. This study found that delayed shipment following FL weaning improves performance under common management conditions for the US cow-calf industry.

Investigating causal biological relationships between reproductive performance traits in high-performing gilts and sows1

Efficient management of swine production systems requires understanding of complex reproductive physiological mechanisms. Our objective in this study was to investigate potential causal biological relationships between reproductive performance traits in high-producing gilts and sows. Data originated from a nutrition experiment and consisted of 200 sows and 440 gilts arranged in body weight blocks and randomly assigned to dietary treatments during late gestation at a commercial swine farm. Reproductive performance traits consisted of weight gain during late gestation, total number born and number born alive in a litter, born alive average birth weight, wean-to-estrous interval, and total litter size born in the subsequent farrowing. Structural equation models combined with the inductive causation algorithm, both adapted to a hierarchical Bayesian framework, were employed to search for, estimate, and infer upon causal links between the traits within each parity group. Results indicated potentially distinct reproductive networks for gilts and for sows. Sows showed sparse connectivity between reproductive traits, whereas the network learned for gilts was densely interconnected, suggesting closely linked physiological mechanisms in younger females, with a potential for ripple effects throughout their productive lifecycle in response to early implementation of tailored managerial interventions. Cross-validation analyses indicated substantial network stability both for the general structure and for individual links, though results about directionality of such links were unstable in this study and will need further investigation. An assessment of relative statistical power in sows and gilts indicated that the observed network discrepancies may be partially explained on a biological basis. In summary, our results suggest distinctly heterogeneous mechanistic networks of reproductive physiology for gilts and sows, consistent with physiological differences between the groups. These findings have potential practical implications for integrated understanding and differential management of gilts and sows to enhance efficiency of swine production systems.

Generalized additive mixed model on the analysis of total transport losses of market-weight pigs1

Transportation losses of market-weight pigs are an animal welfare concern, and result in direct economic impact for producers and abattoirs. Such losses are related to multiple factors including pig genetics, human handling, management, and weather conditions. Understanding the factors associated with total transport losses (TTL) is important to the swine industry because it can aid decision-making, and help in the development of transportation strategies to minimize the risk of losses. Hence, the objective of this study was to investigate factors associated with TTL on market-weight pigs in typically field conditions for Midwestern United States using a generalized additive mixed model (GAMM). The final quasi-binomial GAMM included the fixed (main and interactions) effects of abattoir of destination, type of driver, average market weight, distance traveled, wind speed, precipitation, and temperature-humidity index (THI), as well as the random effects of truck companies and the combination of site of origin and period of the year. Results indicate significant associations between TTL and the main effect of all explanatory variables (P < 0.05), except for wind speed and precipitation. Interactions of average market weight × abattoir, and wind speed × precipitation were also significant. A complex nonlinear relationship between TTL and model covariates were observed for distance traveled, THI, and interaction terms. This study showed that TTL of market-weight pigs are caused by a complex system involving multiple interacting factors, which can be potentially managed to mitigate the risk of losses. In addition, the GAMM showed to be a simple and flexible approach to model TTL because it can capture nonlinear relationships, handle non-normal data, and can potentially accommodate data structure.

Postpartum supplementation of fermented ammoniated condensed whey improved feed efficiency and plasma metabolite profile

Postpartum dietary supplementation of gluconeogenic precursors may improve the plasma metabolite profile of dairy cows, reducing metabolic disorders and improving lactation performance. The objective of this trial was to examine the effects of supplementation with fermented ammoniated condensed whey (FACW) postpartum on lactation performance and on profile of plasma metabolites and hormones in transition dairy cows. Individually fed multiparous Holstein cows were blocked by calving date and randomly assigned to control (2.9% dry matter of diet as soybean meal; n = 20) or FACW (2.9% dry matter of diet as liquid GlucoBoost, Fermented Nutrition, Luxemburg, WI; n = 19) dietary treatments. Treatments were offered from 1 to 45 d in milk (DIM). Cows were milked twice a day. Dry matter intake and milk yield were recorded daily and averaged weekly. Individual milk samples from 2 consecutive milkings were obtained once a week for component analysis. Rumen fluid was collected (n = 3 cows/treatment) at 4 time points per day at 7 and 21 DIM. Blood samples were collected within 1 h before feeding time for metabolite analysis and hyperketonemia diagnosis. Supplementation of FACW improved feed efficiency relative to control; this effect may be partially explained by a marginally significant reduction in dry matter intake from wk 3 to 7 for FACW-supplemented cows with no detected FACW-driven changes in milk yield, milk protein yield, and milk energy output compared with control. Also, there was no evidence for differences in intake of net energy for lactation, efficiency of energy use, energy balance, or body weight or body condition score change from calving to 45 DIM between treatments. Supplementation of FACW shifted rumen measures toward greater molar proportions of propionate and butyrate, and lesser molar proportions of acetate and valerate. Cows supplemented with FACW had greater plasma glucose concentrations in the period from 3 to 7 DIM and greater plasma insulin concentrations compared with control. Plasma nonesterified fatty acid and β-hydroxybutyrate concentrations were decreased in cows supplemented with FACW compared with control cows in the period from 3 to 7 DIM. These findings indicate that FACW may have improved the plasma metabolite profile immediately postpartum in dairy cows. Additionally, supplementation of FACW resulted in improved feed efficiency as accessed by measures of milk output relative to feed intake.