bluuebunny/crossref_metadata_2025_split huggingface dataset:
120 Cross-validation of breeding values and future phenotypes for heifer pregnancy in Red Angus cattle using the LR method
Authors: Giess Lane K , Speidel Scott E , Upperman Lindsay R , Boldt Ryan J , Shafer Wade R , Enns R Mark 
Published: September 2024

Abstract
Heifer pregnancy (HP) in beef cattle is a heritable and economically relevant trait but is challenging to predict using best linear unbiased prediction (BLUP) methodology due to the binary nature of the phenotypes. The observed categorical responses (e.g., 1 = pregnant; 0 = non-pregnant) are due to an animal either exceeding a particular threshold for pregnancy or not on an underlying genetic distribution which is why this binary trait is commonly evaluated using a threshold model (TM). However, TM are susceptible to scenarios where only 1 category of observation is predominant. In this study we compare genetic evaluations including “partial” and “whole” data to cross-validate methodologies for the prediction of HP. The objectives of this study were then to evaluate estimators of prediction accuracy, bias, and dispersion. Heifer fertility data were obtained from the Red Angus Association of America. Evaluations for HP were performed using ASREML3.0 and a univariate, BLUP, traditional TM; and a linear continuous BLUP animal model (LM) on both reference (whole) and validation (partial) datasets. Reference data included all animals with HP phenotypes, and validation data had censored the most recent 5 yr of HP phenotypes (~16% of HP phenotypes). Reference and validation estimated breeding values (EBV) were then compared using linear regression (LR) methods. Heritability estimates were 0.05 (± 0.007) and 0.15 (± 0.009) for LM and TM respectively. The average BIF accuracy of censored validation animals (n = 10,175) using a LM on whole and partial datasets were 0.07 and 0.03 respectively, and using a TM on whole and partial datasets were 0.09 and 0.04 respectively. Comparing the mean EBV from the partial and whole datasets can be a good estimator of bias in the model as the difference is expected to be 0. The difference between the mean EBV from partial and mean EBV from whole datasets were –0.003 and –0.016 for LM and TM respectively, suggesting that the TM is a slightly more biased evaluation. The regression of EBV obtained with whole data on EBV estimated with partial data has an expected value of 1 if there is no over/under dispersion which can be a useful tool in determining model correctness and gauge bias in an evaluation. The closer a regression coefficient is to 1, the less biased the evaluation is. The slope of the regression of EBV estimated from whole data on partial data for validation animals were 0.98 (P &lt; 0.0001) and 0.91 (P &lt; 0.0001) for LM and TM respectively. Although both regression coefficients were above 0.90 suggesting both evaluations are performing well, these results suggest that TM models may be a more biased predictor of HP than LM despite a small benefit in prediction accuracy for the trait.
114 Accuracy of genomic predictions using single and multiple-trait machine learning methods in Canadian beef cattle population
Authors: Li Hongwei , Wang Yining , Vinsky Michael , Valente Tiago , Basarab John A , Li Changxi 
Published: September 2024

Abstract
The advancement in various machine learning (ML) methods provides tools to extract features from a large data set of complex traits and to predict the outcome of the target trait. In this study, we assessed the genomic prediction accuracy using single trait models based on kernel ridge regression (ST_KRR) and linear support vector regression (STLinearSVR) for female feed intake, feed efficiency and fertility traits of Canadian crossbreed beef cattle (n = 2,834 genotyped with 83,875 single nucleotide polymorphisms) and compared their prediction performances to a single trait genomic best linear unbiased prediction (STGBLUP) method. We also evaluated the performances of multiple-trait genomic prediction methods including MAK-based KRR, MAK-based LinearSVR (MAK_MTLinearSVR), and multiple-trait genomic best linear unbiased prediction (MTGBLUP). For the single trait methods, we found that the ST_KRR model was 1.86% to 26.86% more accurate for feed intake and fertility traits including residual feed intake adjusted for backfat thickness (RFIfat), daily dry matter intake (DMI), feeding event duration (DUR), age of first calving (AFC), pre-breeding backfat at first parity (PBBF), and pre-breeding weight at first parity (PBWT) than the STGBLUP method, which had an average accuracy of 0.39 for the traits investigated. For growth and development traits including julian date of birth (JulianDt), weaning weight adjusted to 200 d (WT200d), and birth weight (BRWT) of heifers, STLinearSVR yielded a 5.44% to 9.92% greater accuracy than STGBLUP. As for the multiple trait methods, MAK_MTLinearSVR had a 1.1% to 20.42% greater accuracy for PBWT, AFC, WT200d, DUR, RFIfat, and BRWT than the single trait model of STLinearSVR, while MTGBLUP had a 0.42% to 32.64% greater accuracy for AFC, RFIfat, WT200d and PBBF than the single trait model of STGBLUP. Our results demonstrate the potential application of ML-based multiple-trait models in beef cattle to improve the effectiveness of genomic selection programs, in particular for traits with low heritability.
201 Transcriptome analysis of bovine abomasal mucosa following experimental infection with Ostertagia ostertagi
Authors: Boschiero Clarissa , Liu George E , Tuo Wenbin 
Published: September 2024

Abstract
Ostertagia ostertagi is a cattle stomach nematode that causes significant disease; however, little is known about host responses to infection. Due to the emergence of drug resistance in these parasites, there is a need for alternative treatments. To understand host responses to O. ostertagi infection in the gastric mucosa, gene expression in fundic and pyloric mucosa was compared between infected and uninfected calves for 21 d post-infection. The number of differentially expressed genes (DEGs) increased over time with more upregulated than downregulated DEGs at each time point. Fundic mucosa had more DEGs than pyloric mucosa across all time points. The largest changes occurred between d 7 to 9 and 10 post-infection. Most DEGs are associated with immunity, cellular reorganization, cell migration, and proliferation. Tuft/epithelial cell response to the infection was atypical, lacking key cytokines. Numerous genes associated with T cell exhaustion were upregulated. The data collectively indicate that O. ostertagi infection elicited host immune responses, yet also suggest parasite-induced immunosuppression is present. This may explain why cattle are slow in developing protective immunity to O. ostertagi. Understanding mechanisms of parasite evasion will facilitate the rational design of protective vaccines against complex nematode parasites.
277 Estimating the potential effect of Mycoplasma hyopneumoniae infection on swine sustainability
Authors: Krebs Shelby , Pieters Maria , Schwartz Mark , Urriola Pedro E 
Published: September 2024

Abstract
Mycoplasma hyopneumoniae is the primary causative agent of enzootic pneumonia, one of the most common bacterial pathogens affecting pigs and the main contributor to respiratory comorbidities. Infection with M. hyopneumoniae, commonly observed in growing pigs, results in decreased feed intake and an increase in the number of days to reach market weight. Based on extended days to market, pigs infected with M. hyopneumoniae will have a greater life cycle carbon emissions and water usage than that of non-infected pigs. However, the magnitude of additional carbon footprint and water use in pigs infected with M. hyopneumoniae has never been calculated. Therefore, the objective of this study was to estimate the potential variation in carbon emissions and water footprint generated by M. hyopneumoniae infected pigs. This study was conducted using data from previous publications on M. hyopneumoniae infected pigs in experimental and commercial conditions. The carbon footprint and water usage of pork production was obtained from the literature and was used as a baseline (3,470 kg of CO2 eq and 1,678 m3 water eq; both per 1,000 kg of pork carcass weight). The change in average daily gain was estimated and additional days on feed to reach market weight were used to calculate potential carbon and water impact for pigs infected with M. hyopneumoniae. The estimated carbon emissions and water usage of M. hyopneumoniae infected pigs increased in a range of 84.69 to 142.93 kg of CO2 eq/1,000 kg of pork carcass weight and 40.95 to 69.12 m3 eq/1,000 kg of pork carcass weight respectively, compared with the carbon emissions of non-infected pigs (Table 1). Results of this study showed an increased carbon footprint for M. hyopneumoniae infected pigs by 2 to 4% and water usage increased by 2.5 to 4.1% suggesting that the sustainability of pork production was negatively affected by this bacterial infection. Previous literature on the impact of controlling vaccine-preventable diseases has shown similar results for other swine respiratory pathogens. In addition, these data only included M. hyopneumoniae infected pigs, thus the effect of respiratory co-infections was not estimated and the impact on sustainability metrics may be greater than currently calculated. The application of sustainable practices in animal production, including disease prevention, is key to ensuring a secure food supply for future generations. The carbon and water footprints of swine production are measurements of sustainability, with average daily gain being an important factor.
16 Overview of trace minerals and considerations in defining their requirements
Authors: Spears Jerry W 
Published: September 2024

Abstract
At least eight trace minerals are classified as essential for beef cattle, based on identification of one or more metabolic functions. Essential trace minerals are under homeostatic control mechanisms that alter their absorption and/or excretion, resulting in tissue concentrations of most minerals being maintained within a fairly narrow range. Without whole body homeostatic mechanisms to control mineral concentrations in the body, it would be extremely difficult to formulate bioavailable trace mineral levels in diets within a range that prevents both deficiencies and toxicities. Cellular homeostasis is also important in preventing adverse effects of free metal ions, especially iron and copper, in the cell. Trace mineral requirements are estimated by the National Academies of Sciences Committee on Nutrient Requirements of Beef Cattle. Requirements are based on the concentration of each trace mineral necessary to maximize overall performance (growth, reproduction, and health), and are based on published research. A number of factors can affect requirements of certain trace minerals such as bioavailability, which is affected by antagonist and trace mineral source. There is little recent research on trace mineral requirements. Most recent trace mineral studies have not included a negative control treatment and have evaluated adding additional concentrations of trace minerals to a diet already formulated to meet or exceed NASEM (2016) recommendations. Much of the older trace mineral research was conducted with British cattle breeds. Research has indicated that Continental and Bos indicus breeds differ in regard to copper and possibly selenium metabolism. Trace mineral requirements of breeds that have been developed by crossing Bos indicus with Bos taurus are largely unknown. There have been genetic improvements over time that have resulted in heavier calf weaning weights, faster and more efficient feedlot gains, and heavier slaughter BW. These genetic improvements have resulted in improved energy efficiency. It is unclear if the improved energy efficiency has also been associated with enhanced trace mineral utilization. Use of more aggressive implant programs and beta-agonists in recent years has also improved growth rate and efficiency of feedlot cattle. Well-designed studies are needed to more accurately define trace mineral requirements for beef cattle.
22 Effects of trace mineral source and chromium propionate supplementation on rumen fermentation, growth performance, and carcass characteristics in finishing beef steers
Authors: Heldt Jeff S , Loh Huey Yi , Spears Jerry W , Lloyd Karen , Engle Terry E 
Published: September 2024

Abstract
Crossbred beef steers [n = 400; body weight (BW) = 370 ± 8 kg] were used to evaluate the effects of trace mineral (TM) source and chromium propionate (Cr) on rumen fermentation characteristics, plasma glucose and mineral concentrations, performance, and carcass characteristics in feedlot steers fed a steam-flaked corn-based finishing diet. Steers were blocked by initial BW and randomly assigned within block to 1 of 4 treatments (10 steers/pen) with 10 pens per treatment. The experimental design was a randomized complete block design with a 2 x 2 factorial arrangement of treatments. Factors included: 1) TM source [sulfate or hydroxychloride (IntelliBond] Cu, Mn, and Zn TM supplemented at 18, 40, and 90 mg/kg DM, respectively) and 2) with or without supplemental Cr (KemTRACE) at 0.0 or 0.25 mg/kg DM. Steers were individually weighed on d -1 and 0 and every 28 d throughout the experiment. Jugular blood samples and rumen contents were collected from 10 steers per treatment on d 28 and 84 of the experiment for plasma glucose and TM concentration and volatile fatty acid analysis, respectively. On d 154 of the experiment, steers were harvested at a commercial abattoir and carcass data was collected. Data were analyzed on a pen mean basis for a randomized complete block design using PROC MIXED of SAS. There was no TM source by Cr supplementation interactions for any of the response variables measured, therefore only main effects are reported. Overall ADG (P = 0.03) and gain:feed (P = 0.02) were greater in steers receiving supplemental Cr when compared with steers not supplemented with Cr. Hot carcass weight (P = 0.04), dressing percentage (P = 0.01), longissimus muscle area (P = 0.03), and USDA yield grades (P = 0.04) were greater in steers receiving hydroxychloride TM compared with steers receiving sulfate TM. Steers supplemented with Cr had a greater dressing percentage (P = 0.01) and longissimus muscle area (P = 0.04) compared with steers not supplemented with Cr. On d 28 of the experiment, ruminal acetate concentrations were lesser (P = 0.01) and ruminal propionate concentrations tended to be greater (P = 0.12) in steers receiving hydroxychloride TM compared with steers receiving sulfate TM. Steers supplemented with Cr had greater ruminal acetate concentrations (P = 0.04) and plasma glucose concentrations (P = 0.05) on d 28 of the experiment when compared with non-supplemented controls. These data indicate the Cr supplementation and TM source can influence feedlot steer performance, carcass characteristics, and rumen fermentation characteristics.
436 Regulation of brain-placental axis in mouse versus pig
Authors: Behura Susanta K 
Published: September 2024

Abstract
Emerging evidence suggests that the placenta has key roles in the development of mammalian brain. The brain-placental axis refers to the molecular and cellular events by which the placenta programs the fetal brain development during reproduction and leaves a lasting influence on the health and disease of the brain later in life. Though most studies on the brain-placental axis have utilized mouse models, the pig, Sus scrofa, is now increasingly used as a large animal model to study brain diseases in humans. However, no study has been performed to understand the regulation of the brain-placental axis in a comparative manner between mouse and pig. In the present work, we performed a comparative analysis of single-nuclei gene expression patterns in the placenta and fetal brain between mouse and pig. The placenta and fetal brain cells expressing the common orthologous genes and the species-specific genes were identified in both species. The analysis showed that a relatively fewer number of cell clusters expressed genes in a correlated manner between the placenta and fetal brain of pig relative to that of mouse. The results further showed that specific genes related to visual perception were expressed in specific cell types of the fetal brain of both mouse and pig. These genes were expressed in a coordinated manner with a set of genes expressed in specific cell types of the placenta. Further analysis showed that these placental expressed genes were significantly differentially regulated (P &lt; 0.05, fold changes &gt; 2) in the term-placenta between nocturnal and diurnal animals. Significant enrichment (P &lt; 0.05) of specific binding motifs of known transcription factors, whose functions are related to the specification of retinal cells, was observed in the immediate upstream region of these placenta genes. Phylogenetic analysis of these genes among 29 diverse mammalian species differing in placenta type and activity (nocturnal or diurnal) was performed. The Bayes Traits discrete trait correlation test using the inferred phylogenies and the known trait data identified genes associated with the correlated evolution (Log Bayes Factor &gt; 2) of placenta with animal activity (nocturnal or diurnal). The functional association of these genes with visual perception was evident from differential expression in the ocular cells between pig and mouse. Together, the findings of this study show that the regulation of the brain-placental axis plays a role in the evolution of visual perception function of brain to shape the nocturnal or diurnal activity of placental animals. However, factors other than the brain-placental axis are also known to influence temporal changes in nocturnal or diurnal activity of specific animals. Thus, future studies, potentially applying experimental evolution approaches, are needed to dissect the mechanisms of nocturnal bottleneck in placental animals.
33 Beyond bacteria: Impact of live yeast as a probiotic on the intestinal health of dogs
Authors: Bastos Taís S , Souza Renata B , Leseaux Achraf A , Felix Ananda P 
Published: September 2024

Abstract
Inactivated yeast and yeast-based products are commonly used in pet food to improve palatability, contribute to dietary protein content, and improve gastrointestinal functionality. However, the use of viable yeast Saccharomyces as a probiotic may contribute to additional beneficial effects on dogs and cats. Considering that, in this presentation, we will focus on the use of viable yeast as a probiotic for dogs. A study conducted at the Federal University of Parana, Brazil, observed that Beagle dogs supplemented with a probiotic yeast presented reduced fecal concentrations of total biogenic amines, ammonia, and aromatic compounds and greater fecal concentrations of butyrate. The supplemented dogs also presented an improvement in dysbiosis index, a greater abundance of Bifidobacterium and Turicibacter, and a reduced abundance of Escherichia coli in feces. In addition, control group dogs presented upregulation in microbial genes related to virulence factors (such as lipopolysaccharide export system), antibiotic resistance, and osmotic stress, compared with the probiotic group. These results may indicate a possible protective effect of the yeast probiotic against potential pathogenic bacteria in the gut. The mechanisms by which yeast probiotics may contribute to gastrointestinal functionality in dogs and cats are not fully elucidated. However, they are usually attributed to the stimulation of brush edge disaccharidases; competition for adhesion sites against potential pathogens; stimulation of nonspecific immunity; neutralization of toxins; and direct effect against potentially pathogenic microorganisms. Many of these mechanisms are influenced directly by yeast cell wall components, such as mannans and beta-glucans. One of the main mechanisms of action of mannans is the elimination of bacteria with pathogenic potential that present type-1 fimbriae, such as some strains of E. coli and Salmonella, preventing their adhesion and colonization to the host mucosa. This may also contribute to the establishment of beneficial bacteria in the gut. We can conclude that viable yeast Saccharomyces as a probiotic may have promising beneficial effects on intestinal functionality of dogs.
30 Microbiota and Companion Animal Health
Authors: Suchodolski Jan S 
Published: September 2024

Abstract
The intestinal microbiota has been shown to have an important role in health and disease of animals. It is a complex system that depends on interactions between the luminal environment and specific bacterial taxa and their function (e.g., production of short-chain fatty acids, conversion of bile acids). Dietary substrates are an important factor for microbial metabolism and supplements have the potential to help in maintaining intestinal health. Major changes in the microbiota and their loss of function (dysbiosis) are mainly associated with antibiotic treatment and in chronic intestinal disease likely due to chronic remodeling of the epithelium. Therefore, often these changes persist long-term. Chronic enteropathies (CE) occur very commonly in dogs and cats, and are frustrating to treat due to lack of specific markers. The pathophysiology is complex and includes changes in the immune system (e.g., inflammation), intestinal function, and the intestinal microbiome. The current classification based on treatment response (i.e., food- vs. steroid-responsive) is currently being questioned, as new research findings indicate that CE is a syndrome with many overlapping unspecific features, often with chronic irreversible changes in intestinal function and dysbiosis. The presentation will summarize novel research about the pathophysiology and novel concepts in multi-modal therapy to these conditions. This program will help better understand the role of the intestinal microbiota in health and disease (with focus on acute diarrhea and chronic intestinal inflammation). New diagnostic methods for evaluation of the intestinal microbiota will be covered. Finally, this lecture will review how to best manage the clinical signs of acute and chronic diarrhea. This includes new evidence of the negative impact of antibiotics on the microbiome and the critical role nutrition can play in managing these patients.