bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSIII-A-14 Lysophospholipids Supplementation Increases Growth Performance and hot Carcass Weight in Finishing Beef Steers
Authors: Junior Jose Oliveira , Kwon Eric , McCann Joshua C 
Published: September 2022

Abstract
The objectives were to evaluate the effects of lysophospholipids supplementation on growth performance and carcass traits of finishing beef steers. Simmental x Angus steers (n = 126; BW 246 ± 30.8 kg) from two contemporary groups were utilized in a randomized complete block design. Steers were blocked by BW, stratified by sire and source herd, and allotted into 21 pens with 6 steers each. Pens (7 pens per treatment) were randomly assigned to 1 of 3 dietary treatments: 0 g (LPL0), 5 g (LPL5) or 10 g (LPL10) of lysophospholipids per steer daily (Lipidol® Ultra; Pathways Intermediates USA, LLC). Treatments were delivered via a ground corn-based supplement (0.45 kg/hd) which was added to a dry rolled corn-based finishing ration fed in GrowSafe bunks. After 210 days, steers were slaughtered at a commercial abattoir. Data were analyzed using MIXED procedure of SAS 9.4 with fixed effects of dietary treatment and block, and random effects of herd source and pen nested within treatment. Overall, final BW was greater (P = 0.01) in steers fed LPL5 (651 kg) and LPL10 (648 kg) compared with LPL0 (627 kg). Moreover, steers fed LPL0 had decreased (P = 0.01) ADG compared with LPL5 and LPL10. No treatment differences were observed in dry matter intake or gain:feed (P &gt; 0.16). Steers fed LPL5 (399 kg) and LPL10 (399 kg) had increased (P = 0.05) hot carcass weight compared with those fed LPL0 (387 kg). Additionally, steers fed LPL10 tended to have a greater (P = 0.06) dressing percentage than LPL5. In conclusion, lysophospholipids fed at 5 or 10 g per steer daily increased growth performance and hot carcass weight in finishing beef steers.
PSVIII-B-15 Potential Involvement of DNA Methylation of First Intron in Transcriptional Regulation During Bovine Subclinical Mastitis Caused by Staphylococcus Aureus
Authors: Wang Mengqi , Laterrière Mario , Dudemaine Pier-Luc , Bissonnette Nathalie , Gagné David , Ibeagha-Awemu Eveline M 
Published: September 2022

Abstract
DNA methylation involvement in the regulation of mammary gland inflammatory defense against pathogens, including Staphylococcus aureus(SA) has been documented. However, the mechanisms are not clear. The possible influence of DNA methylation of first introns (DNA-MeFI) on transcriptional activities during subclinical mastitis was studied by profiling the methylome (whole genome methylation sequencing) and transcriptome (RNA-sequencing) of milk somatic cells from cows(n=15) with SA subclinical mastitis (SACs) and healthy cows (HCs)(n=13), followed by bioinformatics processing with standard tools. The DNA-MeFI was calculated, for each of 19411 genes found as expressed in the samples, by averaging the methylation levels of all CpG sites in the first intron. At genome-wide, the DNA-MeFIs was inversely correlated with gene expression (GE) (Pearson’s r=-0.173, p=1.60×10-122)(Figure 1-A). Similarly, the difference in the DNA-MeFI and GE between SACs and HCs was also inversely correlated (Pearson’s r=-0.149, p=4.25×10-97)(Figure 1-B). Application of machine learning by Gaussian Mixed model (GMM) using scikit-learn in python to the changes of DNA-MeFI and GE between SACs and HCs revealed 2866 outliers (GMM’s p&lt; 0.005) that showed significant changes in the DNA-MeFI and/or GE. 644 genes with &gt;10% difference in DNA-MeFI and |log2FC| &gt;1 in GE were selected and referred to as differentially methylated and expressed genes (DME-genes). 644 DME-genes were significantly enriched in 5 GO terms and 11 KEGG pathways related to diseases and immune functions, including Staphylococcus aureus infection and Natural killer cell mediated cytotoxicity (Table 1). Furthermore, 74.84% DME-genes showed inverse changes in DNA-MeFI and GE. Besides, the DNA-MeFI of 264 DME-genes were found to correlate significantly with their GE (|rho| &gt;0.3, FDR&lt;0.05), including 225 DME-genes(85.23%) with inverse correlations(rho&lt; -0.3, FDR&lt; 0.05). 39 DME-genes with positive correlations were significantly enriched in 21 GO terms mainly related to metabolic processes. In conclusion, the DNA-MeFI possibly participate in the regulation of gene expression during bovine subclinical mastitis caused by SA.
PSVIII-B-9
Effects of Level and Type of Fiber Sources on Feed Intake, Average Daily Gain, Digestion, and Milk Production by Alpine Goats
Authors: Wang Wei , Lourencon Raquel V , Puchala Ryszard , Ribeiro Luana , Gipson Terry A , Goetsch Arthur L 
Published: September 2022

Abstract
Thirty Alpine does and 32 doelings, averaging 45±1.5 days-in-milk, were used in a study with four 4-wk periods to determine effects of level and type of neutral detergent fiber (NDF) sources on feed intake, average daily gain (ADG), digestion, and milk production. The 60C, 50C, 50W20S, and 40W30S diets were 60, 50, 30, and 30% concentrate and 40, 50, 50, and 40% forage, with 20 and 30% soybean hulls in 50W20S and 40W30S, respectively. Diet NDF concentration was 36, 39, 52, and 52% for 60C, 50C, 50W20S, and 40W30S, respectively. Overall dry matter intake (DMI) was highest (P&lt; 0.05) for 60C and 50C, but differences were greater in periods 1 (2.96, 2.76, 2.06, and 2.27) and 2 (2.67, 2.76, 2.18, and 2.35) than in periods 3 (2.60, 2.55, 2.04, and 2.28) and 4 (2.38, 2.32, 2.07, and 2.13 kg/day for 60C, 50C, 50W20S, and 40W30S, respectively; SEM=0.142). There was a three-way interaction in ADG, with values of 31, 32, -22, and -10 for doelings (SEM=15.1) and 8, 0, -22, and -11 g for does consuming 60C, 50C, 50W20S, and 40W30S, respectively (SEM=18.6). Digestion of organic matter after period 4 was 71.3, 71.3, 80.1, and 80.7% (SEM=0.95) and of NDF was 44.7, 48.8, 73.7, and 75.8% for 60C, 50C, 50W20S, and 40W30S, respectively (SEM=1.56). Milk fat concentration was highest (P&lt; 0.05) for 40W30S (2.81, 2.92, 2.85, and 3.13%; SEM=0.051), with raw milk yield similar among treatments (3.10, 2.87, 2.64, and 2.79 kg/day 60C, 50C, 50W20S, and 40W30S, respectively; SEM=0.144). Average milk energy yield was 7.61, 7.20, 6.48, and 7.20 MJ/day (SEM=0.354) and 2.85, 2.90, 3.11, and 3.18 MJ/kg DMI for 60C, 50C, 50W20S, and 40W30S, respectively (SEM=0.130). In conclusion, high-NDF diets may limit feed intake more in mid- than late lactation and restrict ADG of doelings; however, perhaps because of differences in digestibility, they did not significantly affect milk energy yield.
PSVIII-B-13 Machine Learning-Based co-Expression Network Analysis Unravels Fertility-Related Genes in Beef Cattle
Authors: Diniz Wellison , Banerjee Priyanka , Rodning Soren P P , Dyce Paul W W 
Published: September 2022

Abstract
Reproductive efficiency is a critical component of a sustainable cow-calf system. While several studies have identified factors underlying fertility, the genetic mechanisms contributing to this complex trait are still unclear. Our goal was to identify a set of predictive biomarker signatures from transcriptomics data associated with female cattle fertility. We implemented a multi-tiered approach using machine learning (ML) feature selection, gene co-expression network, and functional analysis. To this end, we retrieved public data from the Gene Expression Omnibus database (GEO GSE171577). The RNA-Seq data was generated from uterine luminal epithelial cells of recipient cows sampled on day four before embryo transfer. The data (n = 18 non-pregnant – NP and n = 25 pregnant – P) were analyzed using a standard pipeline based on FastQC, MultiQC, STAR, and DESeq2. Genes with expression values &gt; 0.5 counts per million in 50% of the samples were filtered out. Feature and model selection was implemented through BioDiscML. Further, the PCIT algorithm was used to create gene co-expression networks from 15,039 genes kept after quality control. Our ML approach identified nine genes as predictors of pregnancy status. The genes included: SERPINE3, MRTFA, MEF2B, NAA16, ARHGEF7, PDCD1, FNDC1, ENSBTAG00000054585, and ENSBTAG00000019474. The networks from P and NP cows resulted in five and four thousand significantly co-expressed gene pairs, respectively. We then kept 1,837 pairs with a |r| &gt; 0.7 and were co-expressed with the gene predictors from the ML analysis. Biological processes, such as vasculature development, oxidative phosphorylation, and focal adhesion were over-represented by genes from the P network. We identified immune system development, negative regulation of the biological process, and protein modification over-represented processes in the NP gene network. We have demonstrated the potential of combining different methods to identify fertility-related biomarkers and have provided insights into the complex genomic basis underlying pregnancy establishment in cattle.
PSVIII-B-12 Impact of Ruminal Acidosis on Cattle Energy Metabolism
Authors: Linder Haley F , Li Jiangong , Berger Larry L , Green-Miller Angela R , McCann Joshua C 
Published: September 2022

Abstract
The objective of this study was to determine the impact of a bout of ruminal acidosis on gas emissions of cattle unadapted to a high concentrate diet. Eleven ruminally cannulated steers (body weight = 352 kg ± 27) were blocked into 3 groups based on initial body weight. Prior to the start of the experiment, animals were consuming a forage-based diet as well as adapted to the headbox style respiration chambers. Additionally, prior to the experiment, gas emission data were collected over a 24-hour period when cattle received an ad libitum forage-based diet for use as a covariate in the statistical analysis. For the experiment, steers were moved into headboxes at the conclusion of a 24 hour fast and subsequently received 1 of 2 treatment diets: control (CON), forage-based diet or acidosis (ACID), concentrate-based diet. Steers remained in the headboxes for 48 hours. Gas concentrations from each headbox were collected hourly and analyzed with an infrared photoacoustic gas analyzer. Data were analyzed with the MIXED procedure of SAS 9.4. There was a tendency for a treatment × day effect (P = 0.09) with steers on the ACID treatment consuming 1.95 kg less on day 2 than CON steers. Dry matter intake was affected by day (P &lt; 0.01) with steers consuming 4.35 kg less on day 2. There was an effect of treatment (P &lt; 0.01) with CON steers having a greater ruminal pH than ACID steers. Steers on the ACID treatment had less CO2 emissions (P &lt; 0.01) than CON steers, but there were no observed differences (P ≥ 0.19) in O2 emissions or respiratory quotient. Acidosis decreased dry matter intake and CO2 emissions but not O2 emissions for cattle unadapted to a high concentrate diet.
PSXIII-B-6 Effect of Camera Exposure Time on Image Segmentation and Body Weight Prediction
Authors: Bresolin Tiago , Ferreira Rafael , Dorea Joao R 
Published: September 2022

Abstract
External conditions such as lightness and brightness in a scene might have a tremendous effect on the quality of image acquisition, and this may influence on the prediction of phenotypes of interest. Here we investigated the impact of camera exposure time on the performance of image segmentation and body weight (BW) prediction. Top view depth images were acquired from 84 dairy cows using exposure time automatically defined by the camera (Exp0) given the scene light conditions, and manually set as 1,000 milliseconds (Exp1) and 4,000 milliseconds (Exp4) for all cows. Three images per cow from each experiment (n = 252) had the animal body manually traced. A 10-fold cross-validation (random by cow) strategy was used to train and validate three U-Net networks, one per experiment, for semantic segmentation. The trained segmenters were tested on each experiment dataset using intersection over union (IoU) as an evaluation metric. Biological features (BF) including area, volume, circularity, and major axis length were extracted from the segmented images. BF were used as predictors in linear models to predict the BW, and the models’ performance were evaluated using coefficient of determination (R2). IoU remained constant (0.98) when training U-Net using images from Exp0, Exp1, and Exp4 and testing on Exp0 and Exp1, and decreased (0.92) when testing on Exp4. R2 of 0.79, 0.78, and 0.08 were observed to predict BW when the model was trained using BF from Exp0 and Exp1 and tested using BF from Exp0, Exp1, and Exp4, respectively. Lower R2 (0.33, 0.34, and 0.25, respectively) were observed using BF from Exp4 to train the model and test using BF from Exp0, Exp1, and Exp4. Overall, higher exposure times (Exp4) resulted in poorer segmentation quality and consequently less precise BW predictions.
PSXIII-B-11 Identification of Haplotypes Associated with Fetal Loss in Dairy Cattle
Authors: Kiser Jennifer N , Neibergs Holly L 
Published: September 2022

Abstract
Fetal loss occurs in 4 to 13% of dairy cattle worldwide with a subsequent $487 to $1900 economic loss per pregnancy. Previous studies have identified SNPs associated with fetal loss, but few have investigated haplotypes (DNA that segregates to offspring together) associated with fetal loss. The objective of this study was to identify haplotypes associated with fetal loss in Holstein heifers and cows that conceived to the first insemination. This study consisted of 529 Holstein heifers (470 maintained pregnancies to term while 59 experienced fetal loss) and 517 Holstein cows (490 maintained pregnancies to term while 28 suffered fetal loss). Cattle with fetal loss (cases) were genotyped using the Neogen BovineGGP50 BeadChip (SNPs = 43,938) and cattle that calved at term (controls) were genotyped with the Illumina BovineHD BeadChip (SNPs = 777,962). Cases were imputed to HD density using BEAGLE (4.1). Cases and controls were combined to identify 62,819 haplotypes. Haplotype association tests were run for three populations (heifers, cows, and combined) with a chi-squared Bonferroni (BF) corrected significance of p &lt; 0.05. The haplotype analyses identified 121, 47, and 102 haplotypes associated with fetal loss in heifer, cow and combined populations, respectively. Of these, 37 haplotypes were shared between the heifer and cow populations, 39 between cows and the combined, 76 between the heifers and combined, and 37 across all analyses. Loci identified in the haplotype analyses were compared to loci associated (BF p &lt; 0.05) with fetal loss in a SNP by SNP genome wide association analyses. There were 22 loci shared in heifers, 10 in cows and 21 in the combined population. The use of haplotypes, identified an additional 150 loci associated with fetal loss that can be further characterized for their value in selecting cattle that are less prone to late term abortions.
PSXIII-B-17 Risk of Bovine Respiratory Disease by Pathogen Incidence
Authors: Kiser Jennifer N , Neibergs Holly L 
Published: September 2022

Abstract
Bovine respiratory disease (BRD) affects millions of cattle in the US annually. This study sought to identify commensal pathogens in animals without clinical signs that were predictive of clinical BRD using the Wisconsin Health Scoring (WHS) system. Cases were healthy cattle that were later diagnosed with BRD (WHS ≥ 5.0), positive controls (PC) were cattle that were diagnosed with BRD at the time of initial sampling and negative controls (NC) were those that remained healthy throughout the study (WHS ≤ 4.0). Beef feedlot cattle were sampled in Colorado (CO; cases = 13, NC = 500, PC = 488) and Washington (WA; cases = 5, NC = 499, PC = 506). Preweaned Holstein dairy calves were sampled from California (CA; cases = 73, NC = 1017, PC = 1003) and New Mexico (NM; cases = 25, NC = 381, PC = 376). For each animal, mid-nasal and deep pharyngeal swabs were used to test for nine BRD pathogens. ANOVA testing (P&lt; 0.05) and odds ratios (OR) were calculated for each population. In CO, bovine viral diarrhea virus (P = 0.0001, OR = 13.1) and Histophilus somni (P = 0.008, OR = 4.2) were predictive of cattle that would be diagnosed with BRD while bovine respiratory syncytial virus (BRSV; P = 1.1 × 10-6, OR = 40.8) was most predictive in WA. In NM, BRSV (P = 0.005, OR = 5.8) was also predictive of clinical BRD. No pathogen was predictive of BRD risk in CA. Prevalence of the predictive pathogen was higher (P &lt; 0.05) in cases than in PC cattle suggesting that the incidence of pathogens taken at the time of BRD diagnosis may not reflect the pathogen initiating disease. These results also highlight geographical differences in the incidence of BRD pathogens which should be considered when managing to reduce disease.
PSXIII-B-12 Identifying Gene and Metabolite Signature Patterns by Mining co-Expression Networks for Fertility in Beef Heifers
Authors: Banerjee Priyanka , Rodning Soren P P , Diniz Wellison , Dyce Paul W W 
Published: September 2022

Abstract
Fertility is a multifactorial trait partially regulated by genetics. Despite advances in reproductive biotechnologies, reproductive failure remains a challenge to the beef industry. Thus, we hypothesized that blood profiles would differ at artificial insemination (AI) between heifers that become pregnant or remained open following AI and three cycles of natural service. We applied untargeted-metabolomics (blood-plasma) and RNA-Seq approaches (GEO-GSE103628, peripheral white blood cells) on six AI-pregnant (AI-P) and six non-pregnant (NP) Angus-Simmental crossbred heifers. After quality control, differential expression analyses of genes (DEGs) and metabolites were performed. We identified 38 DEGs and 15 metabolites at different levels between the AI-P and NP groups. Co-expression network and differential connectivity (DK) analyses were performed using the PCIT and Cytoscape software platforms. The significantly correlated gene pairs (|r| &gt; 0.99) were filtered with DEGs. The gene co-expression network analysis identified 17 and 37 hub genes in AI-P and NP, respectively. Genes that gained connectivity in NP included TGM2, TMEM51, TAC3, NDRG4, and PDGFB. Likewise, ENSBTAG00000027962, ENSBTAG00000034871, ENSBTAG00000047816 and CYTH3 were less connected. The DEGs, co-expressed and DK genes were over-represented for oocyte meiosis, Wnt and glucagon signaling pathways, propanoate metabolism and N-glycan biosynthesis in the AI-P. MAPK signaling pathway and ubiquitin-mediated proteolysis were over-represented in NP. The metabolomic analysis identified 18 and 15 metabolite pairs significantly correlated (|r| &gt; 0.9) in AI-P and NP. While ornithine and cysteine were identified as hubs for both AI-P and NP metabolites, allantoic acid, methionine, putrescine, phenylethylamine, kynurenine and xylitol were unique to AI-P. Tryptophan and glutamine were unique to the NP. Tryptophan exhibited a gain in connectivity in NP while allantoic acid had more connectivity in the AI-P. Our findings provide new avenues for fertility research. Further validation of genes and metabolites in a cohort with more animals would establish a framework for early fertility prediction.
PSIII-19 Growth Performance, Carcass Traits, and Meat Quality of Pigs from Divergent Groups for Pork Loin Tenderness
Authors: São José Gabryella Luiza F , Nuñez Amoracyr José C , Brito Luiz Fernando F , Schinckel Allan P , Pereira Vanessa Livian A , Filho Albino Luchiari , Carmo Adriana S do , Cesar Aline , Almeida Vivian V 
Published: September 2022

Abstract
Genetic selection for improved feed efficiency and lean growth in pigs has resulted in reduced intramuscular fat content. The aim of this study was to evaluate growth performance, carcass traits, and meat quality in genetically lean immunocastrated pigs grouped based on divergent Warner-Bratzler Shear Force (WBSF) values. The WBSF values of the longissimus lumborum (LL) muscle were obtained from a previous trial evaluating 4 diets, 6 replicates per diet, and 3 pigs per pen, summing up to 72 Large White immunocastrated male pigs. Pigs (initial BW = 28.44 ± 2.95 kg) were fed diets containing either 1.5% soybean oil (CON) or 3% soybean oil (SO), canola oil (CO), or fish oil (FO) in a 98-d study. The original dataset was used to segregate pigs into 2 treatments: high (5.4 to 4.3 kg) and low (3.8 to 2.8 kg) WBSF. The SO diet did not show extreme values for WBSF and was not included in the resulting dataset, which comprised 2 treatments (high- and low-WBSF), 3 blocks (CON, CO, and FO), and 6 replicates per treatment (12 experimental units). No significant differences were observed for growth performance between WBSF groups. When compared with low-WBSF pigs, high-WBSF pigs tended to have decreased (P = 0.07) backfat thickness and intramuscular fat content in the LL and greater (P = 0.09) carcass lean percentage and cooking losses. Oleic acid concentration was less (P = 0.05) in the LL intramuscular fat of high- than low-WBSF pigs. There were statistical tendencies for decreased (P = 0.06) total monounsaturated fatty acids and increased (P = 0.09) total polyunsaturated fatty acids concentrations in the LL intramuscular fat of high- than low-WBSF pigs. In conclusion, immunocastrated male pigs with tender meat had improved nutritional attributes of pork, with no effects on feed efficiency and carcass traits.
PSIII-18 Effect of Various Adaptogens on the Amino Acid and Fatty Acid Composition of the Longissimus Dorsi Muscle from Kazakh White-Headed Bulls
Authors: Tepavcevich Jela , Khabibullin Ruzel , Mironova Irina , Khabibullin Ilvir , Nikolaeva Lyudmila , Vasilyeva Irina 
Published: September 2022

Abstract
The study aimed to evaluate qualitative characteristics of beef from bulls upon the introduction of plant- and animal-originated adaptogens. Kazakh white-headed bulls were devided into four groups (n=12): group 1 (control) - the basic ration (BR); group 2 - BR + Rhaponticum carthamoides; group 3 - BR + pantocrin; group 4 - BR + drone homogenate. The analyzed components were introduced with drinking water in an amount of 0.01 mL per 1 kg of body weight. Samples of longissimus dorsi muscle from18-month bulls were selected for analysis. The research used gas chromatography to determine the fatty acid composition of beef and capillary electrophoresis to establish the amino acid content. It was found that tryptophan (326.7 mg%) in the beef from group 1 was less by 4.66% (P≤0.05) than in the beef from group 3 and by 5.35% (P≤0.01) than in the beef from group 4. The oxyproline concentration in the beef obtained from the control group was 58.67 mg%. The value is significantly greater (2.43-4.66%) than the indices derived from groups 2-4. The maximum difference (P ≤ 0.01) was observed in group 4 (basic ration + drone homogenate). The analysis of the fatty acid composition indicates an increase in palmitic acid (by 2.8%; P≤0.05), myristic acid (by 3.2%; P≤0.05), myristoleic acid (by 2.1%; P≤0.05) in the beef from group 4 compared to the control. Rhaponticum carthamoides and pantocrin in the ration improved accumulation of alpha-linolenic acid by 1.8 (P&lt; 0.05) and 2.3% (P&lt; 0.05) compared with the control group. Thus, the analyzed adaptogens optimized the fatty acid and amino acid composition of beef in varying degrees. The drone homogenate demonstrated the greatest effect.