bluuebunny/crossref_metadata_2025_split huggingface dataset:
53 Establishing a Pan-Epigenome for Cattle and Sheep
Authors: McKay Stephanie , Murdoch Brenda M , Hagen Darren E 
Published: November 2023

Abstract
Genetic and epigenetic factors contribute towards phenotypic variation in complex traits. Epigenetic modifications can affect transcription and translation and have been shown to influence variation in economically important phenotypes in agricultural species. The onset of pangenomics in livestock species is disconnected from pan-epigenomics and hence lacks a fully comprehensive view of diversity in livestock species. To establish a pan-epigenome for cattle and sheep we are comprehensively characterizing epigenomic conservation and diversity through examination of 5-methylcytosine, 5-hydroxymethylcytosine, histone marks H3K4me3, H3K27ac, H3K4me1 and H3K27me3, open chromatin, chromatin accessibility and n6-methyladenosine in the liver, muscle and prefrontal cortex of Brahman, Angus and Holstein cattle as well as Suffolk, Rambouillet and Katahdin sheep. Finally, comparative epigenomics is being used to identify orthologous regions of the sheep and bovine epigenomes that harbor conserved epigenetic modifications and variants. The establishment of a cattle and sheep pan-epigenome will increase our understanding of how different genomes, epigenomes, and gene products from diverse breeds of cattle and sheep affect a variety of important biological phenotypes, supporting more accurate prediction of traits and improving breeding strategies.
161 A System Dynamics Model of Bovine Respiratory Disease Epidemiology and Prevention Strategies in an Integrated Beef Production System
Authors: Kacheri-Moolan Lijith , Kaniyamattam Karun , Tedeschi Luis O 
Published: November 2023

Abstract
Bovine respiratory disease (BRD) is a complex multifactorial disease that results in more than $1 billion in economic losses for the United States beef cattle industry, accounting for approximately 30% of the total antimicrobial use (AMU) in food animal production systems. The prevalence and production losses due to BRD vary significantly between different production systems, and is influenced by the host, pathogen, and environmental risk factors. These multiple risk factors together have a cumulative effect and will increase the prevalence of the disease if no preventive strategies are implemented in the system. Moreover, the increased AMU to treat BRD results in antimicrobial resistance, further complicating the issue. A linear, event-based solution to address such a complex problem will fail to consider the feedback loops and time delays in the system and may cause unintended consequences that might make the problem even more complex. Hence, we propose a more comprehensive system dynamic model to simulate an integrated beef production system with respect to BRD and predict the dynamic behavior of the system under different preventive strategies currently available to the beef industry. Our conceptual model accounts for host risk factors (auxiliary variables in the model) like age, nutritional status, daily weight gain, prior exposure to pathogens, and genetics. The environmental risk factors such as air quality, transportation, temperature humidity index, overcrowding, and source of animals were also included in the model. The various preventative strategies to reduce the incidence of BRD, including vaccination, biosecurity, adequate colostrum, and nutrition, were also added to the model. The key outcome variables considered were net profitability and AMU. The model simulates multiple scenarios by leveraging the auxiliary variables and can provide information about the system’s net profitability and total AMU. The model explains the interconnected effect of various risk factors associated with BRD in multiple complex scenarios and helps understand the combined effect of adopting various preventive strategies and host-environmental factors in controlling BRD. The initial result from our dynamic model suggests that using a combination of preventive measures and avoiding the selected host-environmental risk factors can minimize AMU while improving profit. The long-term goal of our modeling effort is to enable the beef system stakeholders to make informed decisions and strategies to mitigate the impact of BRD, thereby contributing to improved profitability. Through a systems-thinking approach, our model can contribute to addressing the challenges in BRD management currently faced by the US-based integrated beef production systems.
165 Evaluation of the Use of Prenatal Immune Stimulation on the Ability to Alter Postnatal Immune Function in Weaned Pigs
Authors: Burdick Sanchez Nicole C , Mitchell Ty M , Broadway Paul R , Bowen Brooke M , Davis Emily M , Dobbins Thomas W , Barker Samantha N , Legako Jerrad F , Petry Amy L , Carroll Jeffery A 
Published: November 2023

Abstract
One of the most lacking areas where improvements can be made in swine production is in the area of swine health. This study was designed to determine whether exposure to low dose endotoxin (lipopolysaccharide; LPS) during gestation can enhance immunity to a subsequent LPS challenge in piglets after weaning. Pregnant Camborough sows (parity: 2.6 ± 1.4) were assigned to prenatal immune stimulation (LPS; n = 7; administered 2.5 µg/kg BW LPS i.m. at d 78 ± 1.8 of gestation) or saline treatment groups (CON; n = 7). From the 2 prenatal treatment groups, barrows (n = 17 LPS, 17 CON) were identified at weaning (21 ± 1.3 d of age) to subsequently receive a post-weaning LPS challenge. On d -7, barrows were transported to the USDA-ARS Livestock Issues Research Unit in Lubbock, TX where they were housed in individual pens in an environmentally controlled building with ad libitum access to water and a starter ration. On d -1, pigs were fitted with indwelling jugular catheters and subcutaneous temperature loggers. On d 0, pigs were challenged i.v. with LPS (10 µg/kg BW) and blood samples were collected at -2, 0, 1, 2, 4, 6, 8, 12, and 24 h relative to LPS challenge. Data were analyzed using PROC MIXED in SAS, specific for repeated measures. There was a treatment × time interaction for subcutaneous temperature (P &lt; 0.01), where temperature increased more quickly at 1 and 2 h post-challenge in LPS compared with CON pigs. There was a tendency (P = 0.08) for less change in white blood cells, relative to baseline values, in LPS compared with CON pigs. There was a treatment × time interaction (P = 0.01) for lymphocyte concentrations where concentrations were reduced in LPS compared with CON pigs at 8 h post-challenge. There was also a treatment × time interaction (P = 0.01) for the change in eosinophil concentrations, where there was less change in eosinophil concentrations from 1 to 12h in LPS compared with CON pigs. There was a tendency (P = 0.08) for a treatment × time interaction for serum interleukin-6 (IL-6), where concentrations were reduced in LPS compared with CON pigs at 2h (P = 0.01) and tended to be reduced at 1 and 4h post-challenge (P ≤ 0.11). There was a tendency (P = 0.06) for a treatment × time interaction for IL-8, where concentrations were reduced in LPS compared with CON pigs at 1 and 4h (P ≤ 0.01) and tended to be reduced at 2h post-challenge (P = 0.06). Granulocyte macrophage colony stimulating factor and tumor necrosis factor-α tended (P ≤ 0.08) to be reduced in LPS compared with CON pigs. These data suggest that exposure to endotoxin in utero can influence the postnatal innate immune response to endotoxin. Thus, it is possible to influence the innate immune response of pigs in utero, which may serve as a method to positively influence postnatal immune responsiveness.
106 Using a Novel Direct-Fed Microbial as an Alternative for Tylosin Phosphate to Control Liver Abscesses and Decrease Antimicrobial Use in Finishing Beef Steers
Authors: Hoffman Ashley A , Fernando Samodha C , Wells James E , Woerner Dale R , Manahan Jeff L , Long Nathan S , McDaniel Zach S , Smock Taylor M , Line Dalton J , Broadway Paul R , Carroll Jeffery A , Burdick Sanchez Nicole C , Hales Kristin E 
Published: November 2023

Abstract
Our objective was to evaluate the use of a novel direct-fed microbial as an alternative to antimicrobials to decrease liver abscesses in feedlot cattle. Angus beef steers (n = 240; initial BW = 263 ± 18.0 kg) were used in a randomized complete block design comprised of 3 BW blocks and 3 pen replications per treatment. Experimental treatments were randomly assigned to pen within BW block and consisted of: 1) negative control, dietary supplement contained no tylosin phosphate (NCON); 2) positive control, dietary supplement contained tylosin phosphate (PCON); 3) positive control with tylosin phosphate removed the last 65 d of the feeding period (PCONW); and 4) novel direct-fed microbial fed at 1 g mixture/animal with 1 × 1011 CFU/g (DFM). By design, initial BW did not differ (P = 0.79) among treatments, and at the end of the 59-d receiving period, there were no differences in final BW (P = 0.25). From d 0 to d 30, ADG, DMI, DMI as a percentage of BW, and G:F did not differ (P ≥ 0.21). Likewise, ADG, DMI, DMI as a percentage of BW, and G:F, from d 31 to d 59, were not different (P ≥ 0.30). From d 0 to d 59, there were no differences in ADG, DMI, DMI as a percentage of BW, nor G:F (P ≥ 0.20). During the finishing period, live- and carcass-adjusted final BW did not differ (P ≥ 0.57) among treatments. During the finishing period, there were also no differences in ADG, DMI, DMI as a percentage of BW, or G:F (P ≥ 0.17). Carcass-adjusted ADG, DMI as a percentage of BW, and G:F also did not differ (P ≥ 0.16). Across treatments, no differences in HCW were noted (P = 0.84). Dressing percentage, marbling score, longissimus dorsi (LM) area, 12th-rib fat thickness, and calculated yield grade (YG) were not different among dietary treatments (P ≥ 0.32). Liver abscess incidence and severity were not affected by dietary treatments (P ≥ 0.13). The inclusion of a novel direct-fed microbial in finishing cattle diets did not affect growth performance, carcass characteristics, nor the prevalence of liver abscesses. However, the removal of tylosin phosphate 65 d before harvest numerically resulted in the lowest frequency of severe liver abscesses when compared with steers not fed tylosin phosphate.
104 Development of an Experimental Model to Induce Liver Abscesses in Steers Using an Acidotic Diet Challenge and Oral Bacterial Inoculation
Authors: McDaniel Zach S , Hales Kristin E , Nagaraja T G , Amachawadi Raghavendra G , Lawrence Ty E , Tennant Travis C , Carroll Jeff A , Burdick Sanchez Nicole C , Galyean Michael , Smock Taylor M , Ballou Michael A , Machado Vinicius , Davis Emily M , Broadway Rand 
Published: November 2023

Abstract
The objective of this study was to develop a model for liver abscesses (LA) in Holstein steers by using an acidotic diet or acidotic diet plus intraruminal inoculation of Fusobacterium necrophorum, Salmonella enterica serotype Lubbock, and Truperella pyogenes. Holstein steers (n = 40; initial BW = 84.9 + 7.1 kg) were individually housed and randomly assigned to either a negative control diet (CON), an acidotic diet (AD), or an acidotic diet plus intraruminal inoculation with the bacterial mixture [ADB; (1 × 109 colony forming unit (CFU)/mL of each bacteria]. Steers in AD and ADB were cycled on (3 d) and off (2 d) a high-starch diet 20 days before intraruminal inoculation of ADB. Following inoculation, AD and ADB remained on the acidotic diet for the remainder of the study. Ruminal pH boluses were randomly inserted into 19 steers across treatments to monitor ruminal pH throughout the study. Steers were euthanized and necropsied to record gross pathology on the lung, rumen, liver, and colon. Culture techniques were used to determine the prevalence inoculated bacteria within LA. Quantitative polymerase chain reaction methods were used to quantify F. necrophorum in rumen tissue. Data were analyzed as a completely randomized design with animal as the experimental unit, where an α of ≤ 0.05 determined significance. Liver abscess prevalence was 43% in ADB vs. 0% in AD and CON treatments (P &lt; 0.01). Ruminal damage was 51.1% greater in ADB than in AD and 78.6% greater than in CON (P ≤ 0.05). There were no pathological differences in the lungs and colons among treatment groups (P ≥ 0.14). There was a treatment × time interaction for ruminal pH, where pH decreased below 5.6 in AD and ADB calves during each cycle of the acidotic diet (P &lt; 0.01). The ADB contained a greater concentration of F. necrophorum subsp. Necrophorum and subsp. Fundliforme within rumen tissue (P ≤ 0.03). Of the LA cultured, 100% contained F. necrophorum, 50% S. enterica, and 0% contained T. pyogenes. The F. necrophorum subsp. Necrophorum was phylogenetically typed and identical to the strain (FN-8LI) infused in the bacterial inoculation. These data suggest that acidotic diet in combination with intraruminal inoculation of the bacterial mixture is sufficient to induce liver abscesses and provides insight on possible mechanisms and origins of LA. Further studies are needed to validate these results and determine if this model may be used to study novel intervention methods.
6 Hands-On Iii: Building Digital Twins for Precision Livestock Farming: Data Analytics and Big Data Challenges
Authors: Tao Jian , Mendes Egleu D M , Pi Yalong , Cassity Alyssa , Male Revanth Reddy , Kaniyamattam Karun , Duffield Nick , Tedeschi Luis O 
Published: November 2023

Abstract
Precision livestock farming (PLF) is an emerging field that uses technology to optimize livestock production and management. It involves using sensors, cameras, and other data collection devices to gather information on animal behavior, health, and welfare. A digital twin is a virtual replica of a physical system that can be used for simulation, testing, and optimization. This tutorial will provide an overview of the procedure for creating a PLF digital twin with cameras and sensors. We will discuss the benefits of PLF, the hardware and software components needed, and the steps involved in creating a digital twin. PLF digital twins have a range of potential applications and benefits, including improved livestock health and welfare, increased productivity, and efficiency, and reduced environmental impact. At the end of the tutorial, we will host a roundtable discussion of the potential applications and benefits of PLF digital twins.
181 Effects of Moderate Exercise Regimen on Reproductive Development of Replacement Beef Heifers Reared in Drylots at a High Stocking Density
Authors: Rahmel Logan W , Cooke Reinaldo F , Mackey Shea , Pickett Autumn , Colombo Eduardo , Drewery Mason , Cordero Juan , Daigle Courtney L , Harvey Kelsey M M 
Published: November 2023

Abstract
This experiment evaluated the physiological and reproductive responses of beef heifers reared at a high stocking density and provided with access to an exercise area. Ninety Angus × Brahman heifers were ranked by age (257 ± 2 days), body weight (BW; 216 ± 2 kg), and temperament score on day 0 and assigned to a) 1 of 6 drylot pens (10x14 m pens; 10 heifers/pen) resulting in a stocking density of 14 m2/heifer (DENS), or b) 1 of 3 paddocks (2-ha paddocks; 10 heifers/paddock) resulting in a stocking density of 2,000 m2/heifer (CON). On day 15, 3 DENS pens were randomly selected and given access to an exercise area (DENS-EX) for 1 hour three times weekly. Negligible forage was available for CON heifers, whereas all heifers received the same limit fed diet which averaged 13 kg/heifer daily of a corn-based diet. Heifer shrunk BW was recorded after 16 h of feed and water withdrawal on days -3 and 225 for average daily gain calculation. On day 0, heifers were fitted with a pedometer behind their shoulder and an ear tag (CowManager, Select Sires, Plain City, OH) to record behavioral responses. Each week, pedometer results were recorded, and blood samples were collected for puberty evaluation via plasma progesterone. Heifers from CON had more (P &lt; 0.05) steps per week compared with DENS and DENS-EX, and DENS-EX heifers had more (P &lt; 0.05) steps per week compared with DENS. Heifers from CON spent more (P &lt; 0.05) time ruminating and eating compared with DENS and DENS-EX. No treatment effects (P ≥ 0.12) were detected for heifer BW gain or temperament variables. Heifers from DENS experienced delayed puberty attainment given a greater (P &lt; 0.05) proportion of CON heifers were pubertal by day 98 compared with DENS and DENS-EX, whereas a greater (P &lt; 0.05) proportion of DENS-EX heifers were pubertal by day 154 compared with DENS heifers (treatment × day interaction, P &lt; 0.01). Collectively, results from this experiment demonstrate that providing heifers reared at a high stocking density access to an exercise area does not result in similar reproductive responses as those reared on pasture at a low stocking density. This work is supported by the USDA National Institute of Food and Agriculture (#2021-67015-34083).
21 Beef Cattle and Global Warming
Authors: Rotz Alan 
Published: November 2023

Abstract
Beef cattle production is an important contributor to global warming both nationally and globally. Through a national life cycle assessment, we have determined that the production of beef cattle in the U.S. produces about 243 Tg of carbon dioxide equivalents (CO2e) in global warming with an intensity of 21 kg CO2e/kg of carcass weight. This is about 3.5% of the national inventory of greenhouse gas (GHG) emissions. Globally, the Food and Agriculture Organization (FAO) estimates the direct GHG emissions from all cattle other than dairy and their manure to be about 2,260 Tg or about 4.5% of the total global GHG emission. An important consideration in calculating the contribution of beef cattle is the assumed global warming potentials (GWP) used to relate the warming effect of methane and other compounds to that of CO2. Recommended values have varied over the past 20 years as we learn more about the warming potential of various gases. Values assumed affect published assessments, so it is important to consider the GWP values used when comparing studies. Methane is unique among the major compounds affecting global warming because it has a relatively short life in the atmosphere (half-life of about 8 years). Methane released by cattle and their manure oxidizes in the atmosphere returning the carbon originally fixed by growing plants back to CO2 completing a natural cycle. To better represent the warming effect of methane in the atmosphere, a model called GWP* has been introduced. To use this model, the change in emission rate over time must be quantified. Compared with 50 years ago in the U.S., we are now producing 20% more meat using about 15% fewer cattle. We estimate that the GHG intensity in cattle production has decreased 34%, and the total GHG emission related to beef cattle production has decreased 21% over this period. Considering the change that has occurred, using the GWP* model reduces the global warming impact of U.S. beef cattle by over 50% relative to the use of the commonly accepted current GWP factors. Global change is more difficult to quantify. The FAO estimates that over the past 50 years, the global number of non-dairy cattle has increased about 39% with a 78% increase in meat production and 36% increase in related methane emissions. Applying these data indicates that use of the GWP* model decreases the warming effect of global cattle by about 20%. When making policy decisions to mitigate GHG emissions, it is important to properly represent the relative warming effect of the important greenhouse gases.
41 Genetic Selection for Improved Profit Conditioned on Enterprise-Specific Circumstances
Authors: Spangler Matthew L , Golden Bruce L , Newman Scott 
Published: November 2023

Abstract
Circumstances of producers relative to objectives, economic constraints, and production environments differ substantially. Consequently, the specific path of sustainability differs among beef enterprises. Such a path must take a supply-chain approach, contemplating market (consumer) demands, and firm-level economic costs and returns in both the short- and long- term. Long-term economic returns imply longer-term stewardship of natural resources. Genetic selection is uniquely poised to aid in the pursuit of greater economic and biological efficiency, given it represents a cumulative and permanent source of change. However, it is critical that such change be consistent with the producer-specific sustainability path. Given there are multiple traits that impact economic outcomes economic selection indexes are the appropriate tool. The general form of such indexes has been around for about 80 years, albeit with a less than desirable adoption rate in beef selection decisions. The process of index development can account for known sensitivities to differences in marketing endpoints and current levels of phenotypic performance. Moreover, the time horizon used to determine the economic consequences of a selection decision could differ among enterprises. The choice of planning horizon (PH) is an important, yet often overlooked component of breeding objective and index construction. Shorter PH inherently emphasizes traits that can be fully expressed in the near term whilst longer PH allow more substantial weighting of traits expressed later in life. Misalignment of breeding objectives and selection indexes, as might be the case in using a terminal index to choose sires in a self-replacing herd, or incorrect choice of PH could lead to less profitable genetic selection decisions by increasing mature cow weight and/or de-emphasizing reproductive longevity. Consequently, our objective was to provide examples of how trait emphasis might be altered under different assumptions during selection index development using the web-based tool iGENDEC. Indexes assumed replacement females were retained and terminal animals were retained through harvest. We then compared changes in PH, annual cow variable costs, and phenotypic means of hot carcass weight (HCW). The combined relative emphasis (RE) of mature cow weight (MWT) and stayability (STAY) in the breeding objective was 0, 10, and 22% when planning horizon was 2, 10, and 20 years, respectively. As HCW increased from 318 to 408 kg the RE of STAY increased from 10.9% to 18.7% while the RE of HCW decreased from 43.8% to 28.9%. When annual cow variable costs were $250, $500, and $750 the RE of MWT was 6, 14.9, and 22.5%, respectively, assuming the value of calves sold stayed the same. Collectively, these examples illustrate that incorrect definition of breeding objectives and parametrization of indexes can lead to inappropriate weighting of traits that are drivers of long-term resource use (i.e., MWT and STAY).