bluuebunny/crossref_metadata_2025_split huggingface dataset:
3 Effect of Litter Size and Provision of Supplementary Liquid Milk Replacer During Lactation on Piglet Pre-Weaning Performance
Authors: Willard Naomi C , Moest Nicole K , Vande Pol Katherine D , Olivio Alicia , Shull Caleb M , McKilligan Denny , Ellis Michael 
Published: April 2022

Abstract
Recent increases in litter size in commercial sows have been accompanied by higher pre-weaning mortality (PWM) and lower weaning weights. The objective was to determine effects of litter size and feeding liquid milk replacer during lactation (using an automated feeder) on piglet performance. A split-plot design was used with a 2x2 factorial arrangement of treatments: Milk Replacer (MR; main plot; Unsupplemented vs. Supplemented); Litter Size [LS; sub-plot; Low (2 piglets less than functional teat number) vs. High (2 piglets greater than functional teat number)]. Cross-fostering was carried out at 24 h after birth to create treatment litters with similar gender ratio, proportion of cross-fostered piglets, and average and CV of birth weight. Milk replacer was available from 24 h after birth to weaning. Piglets were weighed on d 1 and 20 (weaning) after birth; all PWM was recorded. Growth data were analyzed using PROC MIXED of SAS; PWM data were analyzed using PROC GLIMMIX. Models accounted for fixed effects of MR, LS, the interaction, and random effects of replicate and replicate by MR interaction. There were no MR by LS interactions (P &gt; 0.05) for any measurement. Supplemented compared with Unsupplemented litters had similar (P &gt; 0.05) litter size at weaning and PWM, but greater (P &lt; 0.05) average piglet and total litter weaning weight (Table 1). The High LS treatment had greater (P &lt; 0.05) litter size and total litter weight at d 1 and weaning, but higher (P &lt; 0.05) PWM and lower (P &lt; 0.05) average piglet weaning weight. In conclusion, supplementing piglets with liquid milk replacer increased weaning weight with no effect on PWM, and increasing litter size above sow teat number had negative effects on both PWM and piglet weaning weight.
5 Effects of Nutrition Plans and Floor and Feeder Space on Growth Performance and Behaviors of 6- to 28-kg Nursery Pigs
Authors: Lu Ning , Vier Carine M , Casserly Ronan , Dritz Steve , Navales Ron A , Cast Wayne R , Wells Danielle , Zaragoza Luis E , Young Malachy , Landero Jose , Gomez Fernando , Stas Nat , Orlando Uislei A 
Published: April 2022

Abstract
The objective was to determine the effects of different nutrition plans and floor and feeder space on growth performance and behaviors of 6- to 28-kg nursery pigs. A total of 1,340 pigs (PIC337×Camborough, initially 5.6±0.19 kg) were used in a 7-week trial, which was divided into 3 dietary phases (Phase1: week1, Phase2: week 2-4, and Phase3: week 5-7). Pens of pigs were weighed, blocked by body weight, and randomly allotted to 1 of 4 treatments in a 2×2 factorial design with 10 pens/treatment. Treatment factors were: 1) nutrition plans that either meet or are below PIC nutrient recommendations (lysine, amino acid to lysine ratios, and phosphorous). Diets meeting PIC recommendations had greater ME concentration by 100-150 kcal/kg; 2) floor and feeder space that either meet or are below PIC recommendations (30 or 37 pigs/pen in Phase 1 and 2, 28 or 35 pigs/pen in Phase 3). Pigs and feeders were weighed, and ear and tail lesions were scored and recorded weekly. Data were analyzed using a linear mixed model in R. There was no evidence of interaction between factors. Overall, pig fed diets containing lower nutrient levels had reduced (P &lt; 0.05) average daily gain (ADG), average daily feed intake (ADFI), and gain to feed ratio. Pigs that were housed with less floor and feeder space had reduced (P &lt; 0.05) ADG and ADFI in the overall period. Less floor and feeder space also resulted in a greater removal and mortality rate (P = 0.02). Pigs fed diets containing lower nutrient levels had increased incidence of ear lesions in week5 (6.06 and 2.55%, P = 0.003), week6 (12.59 and 5.45%, P &lt; 0.001), and week7 (21.22 and 11.22%, P &lt; 0.001). In conclusion, feeding nursery pigs below PIC nutrient recommendations and/or providing less floor and feeder space reduced growth performance, increased ear lesions incidence, and increased the removal and mortality rate.
6 Effects of Plans on Growth Performance and Behaviors of 32- to 128-kg Grow-Finish Pigs
Authors: Lu Ning , Vier Carine M , Dritz Steve , Navales Ron A , Cast Wayne R , Wells Danielle , Casserly Ronan , Zaragoza Luis E , Young Malachy , Landero Jose , Orlando Uislei A 
Published: April 2022

Abstract
A total of 1,900 pigs (PIC337×Camborough, initially 32.0 ± 0.52kg) were used to determine the effects of different nutrition plans on growth performance and behaviors of 32- to 128-kg grow-finish pigs. Pens of pigs were weighed, blocked by body weight, and randomly allotted to 1 of 5 treatments that consisted: TRT1) Single-phase program (30-135kg), standardized ileal digestible (SID) lysine:NE ratio at 107% of PIC recommendation at the mid-point of the weight range (referred as “PIC mid-point recommendation”); TRT2) Single-phase program (30-135kg), SID lysine:NE ratio at 125% of PIC mid-point recommendation; TRT3) Two-phase program (30-75 and 75-135kg), SID lysine:NE ratio at 96% and 106% of PIC mid-point recommendation, respectively; TRT4) Two-phase program (30-75 and 75-135kg), SID lysine:NE ratios at 101% of PIC mid-point recommendation in both phases; TRT5) Four-phase program (30-50, 50-75, 75-100, and 100-135kg), SID lysine:NE ratios at 100% of PIC mid-point recommendation in each phase. Dietary amino acids to lysine ratios were below PIC recommendations in TRT1 and TRT3, and met or were above PIC recommendations in TRT2, TRT4, and TRT5. Pigs and feeders were weighed, and ear and tail lesion were scored and recorded every 2 to 3 weeks. From 32- to 81-kg, pigs fed TRT1 diet had reduced average daily gain (ADG, P &lt; 0.05) and gain to feed ratio (G:F, P &lt; 0.05) compared with all other groups (Table 1). Overall, pigs fed TRT2 diet had the greatest ADG, G:F, and lean percentage (P &lt; 0.05). Pig fed TRT1 diet had a greater overall incidence rate of ear and flank lesions compared with the ones in other treatments (P &lt; 0.05). In the current experiment, grow-finish pigs fed with a single-phase nutrition plan containing lower SID Lys levels and amino acid ratios compared with PIC recommendations had reduced performance during the grower phase and greater overall incidence rate of vices.
20 Trials and Tribulations of Countering Insufficient Sperm Quantity with Sperm Quality, Fertility, Synchrony and Deeper Site of Insemination
Authors: Belstra Brad A 
Published: April 2022

Abstract
Superior tools and techniques for boar semen evaluation, semen preservation and artificial insemination (AI) have helped build industry confidence and competence to reduce sperm per female inseminated without compromising reproductive results. Over the last 30 years, the average number of sperm per AI dose has decreased from about 5 to 2 billion in the US and doses containing 1.5 billion sperm have become common in some other countries. While even more genetic lag can be eliminated by further reduction of sperm dose, the level at which fecundity and fertility loss occurs is not a constant and likely varies between different farms and production systems. In general, uterine delivered sperm doses near or lower than 1 billion tend to reduce litter size and further sperm dose reduction eventually reduces pregnancy rate. Deeper catheter deposition of semen, beyond the uterine body, does not seem to effectively compensate for a limiting quantity of sperm. The exception is that surgical injection of sperm into the oviducts requires much less sperm than intrauterine insemination. Reduction of the AI-to-ovulation interval, from 24 to 8 h for example, does not seem to ameliorate the negative effects of a limiting number of sperm when sperm quality is high. The exception may be that a shorter AI-to-ovulation interval can increase reproductive results when both sperm quantity and quality are limiting. Examples include low boar fertility, advanced semen age, or sperm quality compromised by cryopreservation or sex-sorting. A better understating of boar fertility, the interaction of sub-populations of sperm with the oviductal reservoir and their participation in fertilization is likely requisite to continued reduction of the number of sperm required per female. Technologies that predict or regulate sperm quality, fertility and ovulation could prove useful in the quest to use sperm more efficiently and add value to swine AI.
43 Characterization of the Fecal Virome in Beef Cattle with and Without Antibiotic Exposure
Authors: Tom Wesley A , Wells James , Hales Kristin E , Fernando Samodha C 
Published: April 2022

Abstract
Mitigating the spread of antimicrobial resistance (AMR) has become a top priority globally over the last decade. Thus, understanding how bacterial communities acquire and transfer antibiotic resistance is of upmost importance in identifying intervention points for maintaining antibiotic efficacy. It is well documented that horizontal gene transfer (HGT) via bacteriophage transduction has the potential to shift metabolic flux in bacterial communities, yet phage mediated HGT in feedlot cattle with regard to AMR remains poorly characterized. Here we characterize the viral community of 72 beef cattle, where 36 animals received antibiotic exposure and 36 control animals received no antibiotic exposure throughout the duration of the study. Treatment groups were divided into 9 pens with 4 animals per pen. Fecal samples were collected at 3 timepoints and pooled by pen for viral enrichments. Viral particle enrichment was performed using tangential flow filtration and ultracentrifugation. Viral DNA/RNA was extracted with Zymo Quick-DNA/RNA Viral Magbead extraction kit, and shotgun metagenomic libraries were prepared using NEBNext Ultra II library prep kit for Illumina. Libraries were sequenced on the Illumina HiSeq platform (150bp paired-end reads). Sequencing reads were assembled using MEGAHIT, viral genomes were predicted using Virsorter2 and CheckV, and annotated using VIBRANT. In total, 5,875 viral genomes were predicted from the dataset. 635 of those viral genomes were &gt; 60% complete, and 45 were complete circular genomes. 544 auxiliary metabolic genes (AMGs) were detected across all genomes, spanning 49 metabolic pathways with most genes falling under energy, amino acid, and vitamin/cofactor metabolism. Notably, 25 genes involved in secondary metabolite biosynthesis of vancomycin, validamycin, streptomycin, and monobactams were detected. Results indicate that fecal bacteriophages harbor a wide array of AMGs with diverse metabolic potential, including secondary metabolites potentially involved with AMR. The USDA is an equal opportunity provider and employer.
41 Differential Gene Expression of the Bovine Rumen Epithelial Microbiota During a Sub-acute Ruminal Acidosis (SARA) Challenge
Authors: Anderson Chiron J , Schmitz-Esser Stephan 
Published: April 2022

Abstract
Sub-Acute Ruminal Acidosis (SARA) is a metabolic disorder in dairy cattle characterized by a lowered ruminal pH, as a result of high grain diets. Dairy cows experiencing SARA show decreased milk production and impaired health; thus, SARA has major economic impacts. SARA has been associated with changes in the rumen epithelial microbiota. Previously, we performed meta-transcriptome sequencing on rumen epithelial biopsy samples from 3 fistulated Holstein cows before (baseline) and after switching to high concentrate feed to induce SARA to analyze the gene expression of the rumen epithelial microbiota. In this previous analysis, 1,607 features were detected using the KEGG Ontology reference database, including a wide variety of metabolic genes, as well as stress response, motility, and other functions. However, only 3 features were differentially expressed between baseline and SARA conditions using this approach. Here, we present a re-analysis of the meta-transcriptomics data using an improved bioinformatics pipeline to reveal additional genetic diversity and differentially expressed genes. We performed a de novo transcriptome co-assembly with Trinity, mapped reads to the assembled contigs, used RSEM to determine read counts, and DESEQ2 for detection of differentially expressed genes (Q &lt; 0.05). Features were annotated using EggNOG, providing taxonomic predictions and GO, COG, and KEGG-based functional prediction. Using this method, a total of 76,861 transcripts were assembled, and 4,935 genes were differentially expressed between baseline and SARA conditions, representing a substantial improvement over the previous analysis. Our preliminary analysis indicates high expression levels of central metabolism and housekeeping genes, as well as oxidative stress response genes, and outer membrane proteins among rumen epithelial bacteria. Differentially expressed archaeal genes were primarily upregulated under SARA conditions and included genes involved in methanogenesis. Further analyses are ongoing and will provide insight into gene expression of the rumen epithelial microbiota, and their association with SARA.
42 Genome-wide Association Study of Ovary Characteristics in Admixed Beef Heifers Through Comparative Bayesian Approaches
Authors: Anas Muhammad , Zhao Bin , Bhowmik Nayan , Ringwall Kris A , Dahlen Carl R , Swanson Kendall C , Hanna Lauren L Hulsman 
Published: April 2022

Abstract
Reproductive performance of heifers is a key indicator of herd productivity. The objective was to evaluate markers and genes associated with reproductive tract characteristics through a comparative approach. For this study, 295 admixed beef heifers were examined via transrectal ultrasonography at approximately 13 months of age. Exploratory factor analysis of antral follicular count (count per size, side, and total), length, height and diameter for left and right sides of ovaries, and uterine horn diameter revealed a latent variable that included total antral follicle count and ovary diameters per side (n = 3 traits), termed OVARY. Confirmatory factor analysis produced OVARY values per heifer. Quality controls left 116,133 SNP per heifer for association analyses. A marker window-based univariate approach with OVARY was conducted using an empirical Bayesian approach adjusting for nested population structure using marker frequency differences (Method 1) as well as an MCMC Bayesian approach identifying the fraction of SNP to be included with population structure as a fixed effect (Method 2). SNP with high genetic variance in important windows (PPAW &gt; 0.75) were mapped to their closest gene for enrichment analysis. Using Method 1, 2 genes were found to be associated and enrichment analysis identified SMYD2 contributing generally to epigenetic and transcriptional regulatory pathways and GO terms (adjusted P &lt; 0.05). Using Method 2, 11 genes were discovered to be associated with OVARY (adjusted P &lt; 0.05). Three of 11 genes were involved in neural transduction, cornification, epithelial integrity, and adipogenic pathways and GO terms. Eight of 11 genes were involved in reproductive hormonal signaling, post-natal growth, sex determination and reproductive organs development, embryo implantation, and signaling transduction GO terms. Given this, Method 2 provides better insights towards the association of markers and genes for future selection of admixed beef heifers with overall better reproductive characteristics than Method 1.
10 Deep Learning for Multi-Behavioral Video Classification of Interactive Behaviors of Pigs in Single-Spaced Automatic Feeders
Authors: Han Junjie , Siegford Janice , Colbry Dirk , Lesiyon Raymond , Norton Tomas , Chen Chen , Steibel Juan P 
Published: April 2022

Abstract
Automatic pig feeders record individual feeding behavior traits that can be used in genetic selection. However, these feeders cannot measure how feeding traits are affected by behavioral interactions between animals. Moreover, recording behavioral interactions can improve the estimation of social genetic effects. This motivated our assessment of computer vision to classify 4 types of interactions at the feeder: head-to-body contact (HB) including head knocking, tail biting, pushing, gentle nosing and casual contact between head/ears of a pig with a feeding pig; levering (L) where the feeding pig was lifted from behind by another pig; mounting (M) where the feeding pig was mounted by another pig; and no-contact (NC) when a second pig entered the feeder without touching the feeding pig. Behavior at the feeder was filmed twice, 3 weeks apart, for 2 consecutive days each week in 6 groups of grow-finish pigs (10 per group) housed in pens equipped with FIRE feeders. Video segments that involved 2 pigs in the feeder were selected, and labeled as HB (n=10,114), L (n=925), M (n=1,242) and NC (n=3,398). Due to the sparse data available for training and the complex nature of the behavioral interactions, we utilized pretrained convolutional neural networks for automatic spatial feature extraction followed by long short-term memory for temporal feature extraction from sequences of frames. Focal loss, a loss function that assigns different weights to hard/easily misclassified examples to handle class imbalance problem, was used in this study. Accuracy, recall, and precision of behavior classification were obtained from 5 random cross-validations. The overall accuracy was 0.967±0.002. The average recalls for HB, L, M, and NC were 0.977±0.004, 0.866±0.047, 0.969±0.011, and 0.964±0.009 respectively, while average precisions were 0.976±0.002, 0.901±0.029, 0.956±0.018, and 0.963±0.012. The proposed algorithm accurately classified multiple interactive behaviors in an automated feeding stall from digital videos.
46 An Engineers Perspective on Sensor Development and Future Applications in Livestock
Authors: Pandey Santosh 
Published: April 2022

Abstract
Sensors are essential to collect a wide range of high-fidelity and reproducible data from livestock farms. On one hand, commercial cameras are capable of recording large videos for post-processing and analysis on edge computers. On the other hand, a variety of electronic sensors and microprocessor chips are commercially available to track the posture and movement of animals in livestock farms. There are inherent tradeoffs in developing and adopting the above sensors, including issues with handling the big data, effective noise filtering, computing at the edge, on-farm resiliency, power usage, and infrastructure costs. In this talk, we will discuss these tradeoffs while understanding the needs of different livestock farms in the context of our research in sensor technologies.
44 Development and Application of Novel Phenotyping Technologies to Swine Production and Breeding
Authors: Rathje Tom , Jakubowski Andy , Diaz Iara Del Pilar Solar , Mauch Emily , Walugembe Muhammed , Cross Amanda 
Published: April 2022

Abstract
Advancement within numerous categories of technology are beginning to see application for improving production and genetic advancement in pigs. Digital technologies, particularly video, are creating a step change in improved animal environments, biosecurity, vaccine management and disease intervention. For breeders, video technology creates opportunity to begin assessing animal behavior on a useful scale and to expand the quantity and type of animals measured for growth rate, body composition, structural integrity and feed efficiency. A seemingly endless stream of ‘omics’ data is becoming less costly to obtain and includes such datasets as common SNP arrays in addition to DNA sequence, transcriptome, proteome, metabolome, gut microbiome and more. Leveraging the capabilities of these data to predict a phenotype is key to unlocking the full potential of ‘omics’ data. Novel, at least to animal scientists, analytical techniques are required to understand gene networks and their associated expression profiles. These techniques apply equally to video data, which in its purest form, is an interpretation of complex patterns. Scaling and applying these techniques will be important over the coming decade. There exists today a very applied approach to using these technologies in the swine industry. One of the most complex and well-trained pattern recognition technologies lies within our own brain. Experienced managers reviewing video of pigs within facilities, team members entering and performing critical activities impacting biosecurity and coordinating these observations with simple interventions can make large, positive improvements in productivity. Investing in hardware and time will produce results that reduce stressors, improve processes that protect the farm from pathogens and result in better overall animal well-being. This talk will focus on examples of current applications that are of benefit today. In addition, we hope to promote discussion around priorities for genetic improvement, pig management and the practical needs to move a variety of technologies from research to development in the field.
49 Determining the Phosphorus Release of Grainzyme Phytase in Diets for Nursery Pigs
Authors: Becker Larissa L , Wensley Madie R , DeRouchey Joel M , Woodworth Jason C , Tokach Mike D , Goodband Robert D , Gebhardt Jordan T , Raab R Michael , Lessard Philip 
Published: April 2022

Abstract
A total of 360 pigs (Line 200 × 400, DNA, Columbus, NE, initially 9.9 ± 0.19 kg) were used in a 21-d growth study to determine the available P (aP) release curve for GraINzyme phytase (Agrivida Inc., Woburn, MA). Pigs were weaned at approximately 21-d of age, randomly allotted to pens based on initial body weight (BW) and fed common starter diets. From d 18 to 21 post-weaning, all pigs were fed a diet containing 0.11% aP. On d 21 post-weaning, considered d 0 of the study, pens were blocked by BW and randomly allotted to 1 of 8 dietary treatments with 5 pigs/pen and 9 pens/treatment. Dietary treatments were formulated to include increasing aP derived from either an inorganic P source (0.11, 0.19, or 0.27% from monocalcium P) or increasing phytase (150, 250, 500, 1,000, or 1,500 FTU/kg). Diets were corn-soybean meal-based and contained 1.24% standardized ileal digestible (SID) Lys. On d 21 of the trial, 1 pig/pen (weighing closest to the mean pen BW) was euthanized and the right fibula was collected to determine bone ash using the non-defatted processing method. Overall (d 0 to 21), pigs fed increasing aP from inorganic P or phytase had increased (linear, P &lt; 0.002) ADG, ADFI, and G:F (quadratic, P &lt; 0.05). Bone ash weight (g) and percentage bone ash increased (linear, P &lt; 0.001) with increasing inorganic P or added phytase. The release equations developed for GraINzyme for ADG, G:F, bone ash weight, and percentage bone ash are: aP = (0.255 × FTU) ÷ (1,299.969 + FTU), aP = (0.233 × FTU) ÷ (1,236.428 + FTU), aP = (45,999.949 × FTU) ÷ (462,529,200 + FTU), and aP = (0.272 × FTU) ÷ (2,576.581 + FTU), respectively.