bluuebunny/crossref_metadata_2025_split huggingface dataset:
342 Sow weight development: A pragmatic approach to crossbred and selection populations
Authors: Bergsma Rob , Lei Huaigang , Yang Chengbo , Knol Egbert F 
Published: September 2024

Abstract
Feed used for maintenance in sows is around 1% of their live weight, and a 10 kg greater sow body weight (BW) from first lifetime insemination onwards requires 36.5 kg extra feed for maintenance annually, which increases the feed cost for a 1,000-sow operation unit by approximately $15,000 CAD per year. Genetic selection, through emphasis on feed efficiency, changes body development year after year. Phenotypic sow development should allow for adequate litter weight, litter size and longevity for an optimum lifetime production. In this study we wanted to understand sow mature weight and its variation. Sow BW (n = 14,554 of 5,292 sows) around farrowing and litter weights were collected on two crossbred and one purebred farm with industry accepted feeding protocols; that is, limited feeding at the different stages of production. Sow BW were corrected for stage of gestation and realized litter weights to represent empty BW at the day of farrowing. Body weight at the age of first insemination was added. When estimating genetic parameters, the statistical model for sow BW included, in addition to Line and HerdYearSeason, a rate parameter as a covariate (b1*AGE -1) within Farm. A bivariate analysis applying a repeatability model for the BW of purebred and crossbred animals yielded similar heritabilities (h2 = 0.58 ± 0.05 and h2 = 0.55 ± 0.05, for purebred and crossbred, respectively), and greater relevant genetic variances (335 ± 40 and 166 ± 13 kg2) with a clearly positive, but not significant genetic correlation of 0.49 ± 0.46. The (random) effect of a permanent environment was not significant for either characteristic. A second analysis in which genetic parameters were estimated simultaneously for the plateau and the rate parameter showed that genetic selection based on the repeatability model for BW only, affected both the plateau and the rate parameter. Only crossbreds were included in this analysis because the minimum required BW observations per sow were not met for purebred animals. Selection for mature BW might affect other key traits. The phenotypic correlations between the EBVs for the BW of crossbred sows and litter weight, litter size and longevity were -0.15, -0.02 and +0.02, respectively. Genetically heavier or smaller animals do not have better production with heavier ones possibly having slightly decreased performance. However, if animals are treated as equally and uniformly as possible, it is reasonable to assume that genetically heavier animals use more feed for growth, instead of for reproduction, given equal feeding rations. Heritability estimates point to a clear genetic drive to BW development. This study shows the relevance of weight observations at nucleus level and the necessity to estimate genetic correlations with production traits.
344 Preliminary heritability estimate of liver abscess incidence in beef on dairy heifers
Authors: Zuvich Miranda L , Enns R Mark , Wilson Reese , Woerner Dale R , Theurer Miles , Cleveland Matthew , Speidel Scott E 
Published: September 2024

Abstract
This preliminary study aimed to estimate the heritability of liver abscess incidence in fed, beef on dairy crossbred progeny. Liver abscesses affect approximately 20% to 30% of livers at slaughter. They are commonly identified during viscera inspection at slaughter due to difficulty with antemortem diagnosis. All livers with abscesses are condemned, causing a profit loss for producers. This loss is increased when the abscesses are ruptured or adhered to the gut due to additional condemnation of the gut. The most common prevention techniques include antimicrobial feed additives and nutritional management; however, mitigation has not been highly effective. Few studies have attempted to ascertain if a genetic component for liver abscess incidence exists. Determining if there is a genetic component to liver abscess occurrence could enable the ability to utilize genetic selection as a preventative measure. Liver abscess scores were collected on 1,492 crossbred beef on dairy heifers at slaughter. Cattle were harvested in Kansas. Individual livers were scored using the Elanco scoring system of 0, A-, A, A+. Scores of A+, A+AD, and A+O were combined into the A+ category. A score of 0 indicates a normal liver, as scores of A-, A, and A+ indicate increasing severity of abscesses. Scores of A+AD and A+O represent animals with adhesion to the gut or ruptured abscesses, respectively. In the dataset, the distribution was 903, 168, 69, and 352 for scores of 0, A-, A, and A+, respectively. Overall, the prevalence of liver abscesses was 39.5% in this sample. All 1,492 heifers had recorded sire information, but no dam information existed other than knowing they were of dairy origin. In total, 19 unique sires were represented in the data, with six of the sires producing 89.4% of the heifers. A 3-generation sire pedigree was built from the data, and heritability was estimated using a sire model and the statistical software package ASReml 3.0. Fixed effects included the number of bovine respiratory disease treatments, age in days, and a contemporary group consisting of kill lot and treatment type. These cattle were part of an additional study evaluating the effectiveness of various treatment regimens for mitigating the incidence of liver abscesses. There were three treatment groups, one control and two treatments. Genetic and phenotypic variation for this model was estimated to be 2.70 × 10-7 ± 9.99 × 10-9 and 1.58 ± 5.86 × 10-2, respectively. With such a small genetic variance estimate, the heritability of liver abscesses was effectively 0 (1.70 × 10-7), which suggests the lack of a genetic component for liver abscesses in these data. This was a preliminary study that had limited sire variation. Currently, dam information is being accumulated in an attempt to account for dam genetic variation.
312 Leveraging digital phenotyping from research to implementation: Insights from a pig breeding company
Authors: Chen Ching-Yi , Psota Eric , Valente Bruno , Knap Pieter , Holl Justin W 
Published: September 2024

Abstract
In pig breeding, the integration of phenotypes into genetic improvement has been employed for decades. With today’s advancements in modern sensors, digital phenotyping provides a promising avenue for further enhancing accuracy through genomic selection. This integration also creates opportunities to study areas that used to be challenging due to limitations in data collection. We present four examples of digital phenotypes to illustrate how a company may leverage digital phenotyping for genetic implementation: individual feed intake, computer vision leg scoring, behavior, and metabolomics. Phenotypes recorded using automated electronic devices such as feed intake devices enable continuous tracking and recording of individual feed intake events when animals enter the feeder station during performance testing. The full series of events is often condensed into a single average per individual prior to genetic evaluation. By implementing computer vision, the precision of leg scoring phenotypes has increased from subjective, human-measured categorical scores of 1 to 9 to objective, camera-based continuous assessments. We have implemented convolutional neural networks (CNNs) to predict leg scores in our selection process. Using automation, the camera-based leg scoring system enables us to extend the scale of data used in genetic evaluations to improve animal welfare and longevity. Digital phenotyping holds promise for behavioral studies. Traditional methods of phenotype collection for individual behavior have been hindered by challenges such as the difficulty of capturing individual identification and the time-consuming nature of data collection. We have developed a proprietary, custom ear tag reading method and tracking algorithm that enables the automated identification of unique pigs even in visually challenging conditions. The method estimates behavior traits including time spent eating, drinking, lying, sitting, standing, and meters of distance traveled. These are used for genetic parameter estimation with investigations on association with production traits. Understanding metabolic profiles of pigs offers the potential to uncover new traits that were previously difficult to measure, and to identify biomarkers associated with traits. In conclusion, the integration of digital phenotyping into pig breeding programs offers a path toward more precise and efficient genetic improvement. Digital data capture yields a large amount of data which still provides novel opportunities for research and application.
275 Frequency of chronic passive congestive livers at harvest in the Texas Panhandle and the association with carcass outcomes
Authors: Eckhardt Megan E , Lawrence Ty , Lucherk Loni W , Schwartz Trent 
Published: September 2024

Abstract
Chronic passive congestive (CPC) livers are reported as one of the most common clinical signs of right-sided Bovine Congestive Heart Failure (BCHF). Frequency of CPC livers at harvest and the associated loss of offal and carcass value does not appear in the literature. Our objectives were to 1) quantify the frequency of CPC livers at harvest within the Texas Panhandle, and 2) evaluate the association with offal and carcass outcomes. Audits were performed over the duration of a production week (both harvest shifts) per each large commercial beef processing facility (4 total) in the Texas Panhandle. West Texas A&M University trained personnel identified CPC (large blue) livers at evisceration and documented heart score (HS; scale 1 = normal to 5 = extreme structural changes), liver weight, USDA-FSIS inspection fate (U.S. Inspected & Passed; U.S. Condemned) of the liver, remaining viscera, and carcass. Other visual observations (sex, predominant black hair coat color, carcass/visceral edema, liver abscesses) were noted. 1) Frequency data were documented among cattle-type populations: sex (steers, heifers, cows, bulls), and phenotype [native, dairy-cross, dairy, category-B (Mexico-origin)]. 2) Carcass and lot identification were collected for the purpose of tracking and obtaining carcass grading data. Of carcasses deemed wholesome-U.S. Inspected & Passed, USDA yield and quality metrics [hot carcass weight (HCW), 12th-rib fat thickness (FT), ribeye area (REA), marbling score (MS)] of those identified with CPC, as well as data for the balance of respective lots were collected. Carcass outcomes of those exhibiting a CPC liver were compared with the outcomes of remaining lot. Frequency data were analyzed via chi-square. Carcass data were analyzed using mixed models, where occurrence of CPC liver was the fixed effect; facility, cattle type, and sex were random effects. A total of 83,527 animals were audited, with a CPC liver frequency of 0.17% (n = 144). Frequencies among sex (steer = 0.16%; heifer = 0.17%; cow = 0.33%; P &lt; 0.01) and phenotypes (native = 0.15%; category-B = 0.04%; dairy cross = 0.14%; P = 0.01) were documented. Heart scores ranged from 1 to 4, with HS 3 occurring most frequently [HS 1 (n = 2); HS 2 (n = 39); HS 3 (n = 62); HS 4 (n = 17)]. Weights of CPC livers ranged from 7.3 kg to 34.4 kg; the heaviest CPC livers were recorded in cows (mean = 17.2 kg; P &lt; 0.01). Despite USDA-FSIS guidelines, 2.08% of CPC livers were U.S. Inspected & Passed, along with 16.90% of viscera and 84.03% of carcasses. Cow carcasses encountered the greatest U.S. Condemn-rates (38.24%) among the sex categories. Within the fed-beef population, natives were the only category resulting in U.S. Condemned carcasses (10.64%). All carcass outcomes were decreased (P ≤ 0.01) by CPC livers.
330 Growth performance, incidence of scours, and plasma metabolites in beef × dairy crossbred calves transported at 2, 4, 8 and 14 d of age
Authors: Chibisa Gwinyai E , Konetchy Denise , Chahine Mireille , Murdoch Gordon K , Adams-Progar Amber , Christensen Lauren 
Published: September 2024

Abstract
Transportation can compromise health and production performance in young calves. Although widely accepted that the younger calves are, the greater the probability of negative outcomes, there still is a lack of evidence-based recommendations on the minimum age at transportation. Our objective was to evaluate the impact of transport age on growth performance, incidence of scours, and plasma metabolites over the first 28 d post-transport in Charolais × Holstein crossbred calves. Calves (n = 36) ages 2, 4, 8 and 14-d old were transported in summer from a commercial farm to an on-campus calf rearing facility (410 miles). Calf body weight (BW) was recorded before departure, on arrival and d 28 post-transport. Dry matter intake (DMI) and fecal scores were recorded daily. Blood samples collected prior to transportation, on arrival, and d 7 and 28 post-transport were used for targeted metabolomics analysis (Biocrates MxP Quant 500 kit). Growth performance and fecal score data were analyzed using PROC MIXED (SAS) whereas R was used for predictive modeling of metabolomics data. Over the 28-d period post-transport, DMI was greater (P &lt; 0.01) for 14 d than 2 and 4 d old calves; however, it did not differ between 2, 4, and 8 d old calves. Average daily gain (ADG) and feed efficiency (FE) were also greater (P &lt; 0.01) for 14 d than 2, 4, and 8 d old calves. During wk 1 post-transport, the total number of days calves had scours was least (P &lt; 0.01) for 2 and 14 d, intermediate for 4 d, and greatest for 8 d old calves. During wk 2, the total number of days with scours was less (P &lt; 0.01) for 8 and 14 d (average of 2 d) compared with 2 and 4 d old calves (5 d). Additionally, the total number of days calves had scours during the first 2 wk post-transport tended (P = 0.08) to be greater for 2, 4, and 8 d than 14 d old calves. However, during wk 3 and 4 post-transport, there were no differences (P ≥ 0.58) in the total number of days with scours across transport age. Arginine methylation, d 7 of measurements, carnitine uptake defect, phosphatidic acid 16:0:18:2, methylenetetrahydrofolate reductase, sodium, triglyceride 18:2:34:4, threonine, α-aminobutyric acid, and glycolithocholic acid 3-sulfate were the most important features in terms of predicting the occurrence of scours. Overall, DMI, ADG and FE were less for calves transported at 2, 4, and 8 d than at 14 d of age, which could partially be attributed to differences in the incidence rate of scours. In addition, several plasma metabolites could be good predictors of scours in transported calves.
335 Effects of feeding an immunomodulatory feed additive (NutraGen) on serum cytokine and antibody concentrations in calves following exposure to a combination bovine respiratory disease challenge
Authors: Markey Jazmin A , Rudd Jennifer , Snider Tim , Montelongo Marie , Humphrey Brooke , Chapman James D , Sharman Evin D , Garcia Miriam , Reuter Ryan R , Beck Paul A , Foote Andrew P , Wilson Blake K 
Published: September 2024

Abstract
Two 89-d experiments (Exp 1 and Exp 2) evaluated the effects of feeding an immunomodulatory feed additive (NutraGen; NG) in calves following exposure to bovine viral diarrhea virus (BVDV) on d -3 and Mannheimia haemolytica (MH) infection on d 0. For each experiment, steers [body weight (BW = 251 ± 38.2 kg were randomly allocated to 1 of 3 treatments. Treatments included a placebo (CON; Exp 1 n = 5; Exp 2 n = 5), a placebo fed from d -18 to d -3 followed by NG fed from d -3 to d 28 (CHLG; Exp 1 n = 5; Exp 2 n = 6), and NG fed from d -18 to d 28 (PREC; Exp 1 n = 6; Exp 2 n = 5). Data were analyzed using the GLIMMIX procedure of SAS Version 9.4 (SAS Institute, Cary, N.C.). Animal served as the experimental unit and time served as a repeated measure. Treatment, time, and the treatment × time interaction served as fixed effects. Block was included as a random effect. Cytokine data were tested for normality using the Shapiro-Wilk test, determined to be non-normal, and logarithm (base 10) transformed as a result prior to statistical analysis. Multiple time effects and treatment × time interactions occurred for serum MH, BVDV 1, and BVDV 2 antibody concentrations in both experiments (P ≤ 0.05). In Exp 1, there was a tendency for an overall treatment effect for calves assigned to the CON treatment to exhibit the greatest MH serum antibody concentrations (P = 0.06). While no differences were detected between treatment groups, BVDV 1 and BVDV 2 antibody concentrations peaked on the same day in both experiments, d 28 post-challenge. There were no treatment × time interactions, treatment effects, or time effects for serum TNF-α, IFN-γ, or IL-17A concentrations (P ≥ 0.13) in either experiment. In Exp 1, there was a treatment effect for serum IL-10 (P ≤ 0.0001), where calves assigned to the PREC treatment had increased serum IL-10 concentrations when compared with calves in the other treatment groups. In Exp 2, there was a tendency for a treatment effect for IL-10 concentrations, where calves assigned to the PREC treatment displayed decreased IL-10 concentrations when compared with calves in the other treatment groups (P = 0.07). These data suggest that feeding NG to calves prior to a stress experience may alter cellular responses. Overall, these experiments suggest that NG impacted antibody concentrations and cytokine expression during a bovine respiratory disease challenge.
334 Metagenomic- and culture-based characterization of the ocular microbiome in cattle with infectious bovine keratoconjunctivitis
Authors: Amat Samat , Luecke Sarah M , Holman Devin B , Anas Muhammad , Stokka Gerald 
Published: September 2024

Abstract
Pinkeye, clinically known as infectious bovine keratoconjunctivitis (IBK), is one of the most highly contagious diseases impacting cattle at all ages. Despite extensive use of antibiotics and vaccines targeting Moraxella bovis, the primary IBK pathogen, the incidence of pinkeye has been increasing in North American beef cow-calf operations. This highlights the incomplete understanding of the pathogenesis of this disease and the need for novel and alternative approaches to control IBK. The objectives of this study were to: 1) characterize the ocular microbiome of beef cattle with and without IBK using shotgun metagenomic sequencing; 2) investigate the genetic diversity of M. bovis, Moraxella bovoculi, and commensal ocular bacterial isolates; 3) evaluate whether selected ocular probiotic candidate strains inhibit Moraxella pathogen growth in the presence of the ocular microbiome in culture using qPCR. A total of 143 ocular swabs were collected from cattle with (n = 102) or without IBK (n = 42) and before antibiotic treatment from beef herds across North Dakota, USA. Fifty samples from IBK (n = 38) and healthy cattle (n = 12) were also subjected to shotgun metagenomic sequencing. Seven bacterial species were relatively more abundant (P &lt; 0.05) in the healthy cattle ocular microbiome including Bifidobacterium globosum, Bacillus licheniformis, Pasteurella multocida, Ruminococcus sp900316555, and Ruminococcus sp900100595. Arthrobacter luteus was the only bacterial species significantly associated with IBK-affected cattle. From the metagenomes, 37 high-quality dereplicated metagenome-assembled genomes (MAGs) were recovered, nearly a third of which were identified as Mesomycoplasma bovoculi (n = 10). M. bovis (n = 5) and M. bovoculi (n = 13) were also isolated from the ocular swabs of both healthy and IBK-affected cattle. These isolates represented 9 M. bovoculi and 5 M. bovis strains (average nucleotide identity &lt; 99.99%). We also isolated and sequenced several potentially beneficial bacterial species from healthy cattle including Bacillus pumilus, Lactiplantibacillus plantarum, Lentilactobacillus buchneri, Levilactobacillus brevis, and Weizmannia coagulans. Four of these probiotic candidates were also tested for their inhibitory effects against M. bovoculi in co-culture with the ocular microbiome after 24 h incubation using qPCR. The B. pumilus, L. buchneri, L. plantarum, and W. coagulans strains, as well as a mixture of all four isolates, significantly reduced the growth of Moraxella. In summary, our results provide important information on the culturable and non-culturable fraction of the bovine ocular microbiome potentially associated with IBK and suggest that certain bacterial species in the eye may inhibit the growth of Moraxella spp.
336 Effects of feeding an immunomodulatory feed additive (NutraGen) on metabolite concentrations and cortisol production in calves following exposure to a combination bovine respiratory disease challenge
Authors: Markey Jazmin A , Rudd Jennifer , Snider Tim , Montelongo Marie , Humphrey Brooke , Chapman James D , Sharman Evin D , Garcia Miriam , Reuter Ryan R , Beck Paul A , Foote Andrew P , Wilson Blake K 
Published: September 2024

Abstract
Two 89-d experiments (Exp 1 and Exp 2) evaluated the effects of feeding an immunomodulatory feed additive (NutraGen; NG) in calves following exposure to bovine viral diarrhea virus (BVDV) on d -3 and Mannheimia haemolytica (MH) infection on d 0. For each experiment, steers [body weight (BW) = 251 ± 38.2 kg)] were randomly allocated to 1 of 3 treatments. Treatments included a placebo (CON; Exp 1 n = 5; Exp 2 n = 5), a placebo fed from d -18 to d -3 followed by NG fed from d -3 to d 28 (CHLG; Exp 1 n = 5; Exp 2 n = 6), and NG fed from d -18 to d 28 (PREC; Exp 1 n = 6; Exp 2 n = 5). Data were analyzed using the GLIMMIX procedure of SAS Version 9.4 (SAS Institute, Cary, N.C.). Animal served as the experimental unit and time served as a repeated measure. Treatment, time, and the treatment × time interaction served as fixed effects. Block was included as a random effect. Multiple treatment × time interactions and time effects occurred for serum glucose, lactate, blood urea nitrogen, and non-esterified fatty acid concentrations (P ≤ 0.003) in both experiments. There was a general trend for serum glucose to decrease over time post-challenge, suggesting increased cellular utilization of glucose in response to the challenge. In Exp 1, treatment effects occurred for serum glucose (P ≤ 0.001) and serum lactate (P ≤ 0.01), where calves assigned to the CHLG treatment displayed the greatest concentrations of the metabolites. Blood urea nitrogen concentrations peaked at h 48 in Exp 1 and h 6 in Exp 2. There were no treatment effects or treatment × time interactions for serum cortisol, hair cortisol, or fecal corticosterone concentrations in either experiment (P ≥ 0.17). There were, however, multiple time effects for serum cortisol, hair cortisol, and fecal corticosterone concentrations in both experiments (P ≤ 0.02), indicating that the challenge directly impacted cortisol and corticosterone production. Serum cortisol steadily increased from h 96 to h 168 in both experiments. Trends in cortisol and corticosterone production were similar in both experiments; however, peak concentration times for these variables occurred later in Exp 2. These data suggest that feeding NG to calves may alter glucose availability and nutrient utilization in response to infection resulting from a bovine respiratory disease challenge.