bluuebunny/crossref_metadata_2025_split huggingface dataset:
212 Genome-Wide Association Study Investigating the Genomic Components of Efficiency in Beef Cows
Authors: Radwell Laine T , Delver Justin J , Lardner Herbert A , Penner Greg B , Asai-Coakwell Mika 
Published: November 2023

Abstract
Efficiency of mature beef cows consuming high-forage diets is not comparable with standard definitions of beef cattle efficiency such as feed conversion or residual feed intake in the feedlot setting. This study aimed to conduct a genome-wide association study (GWAS) to identify regions of the bovine genome associated with efficiency in mature beef cows. Ninety-eight black Angus cows were managed under extensive feeding programs over a two-year period. Using rump fat at calving, calving date, and calf weaning weight as a percentage of the body weight of the dam, a weighted percentile scoring system was used to rank efficiency. Eighty-three of the cows were retained for the GWAS. The 20 most and 20 least efficient cows (HD dataset, n=40) were genotyped with the Illumina BovineHD BeadChip (777,000 SNPs) while the remaining cows were genotyped with the Neogen GGP Bovine 100K chip (LD dataset, n = 43). The LD dataset was imputed to the HD SNP array density using Beagle5.4 (FULL dataset, n = 83). Three separate GWAS were conducted using GAPIT (version3). The first GWAS was performed on the HD dataset using a quantitative phenotype determined by the ranking system. The second GWAS was performed with the HD dataset using a qualitative phenotype (efficient vs non-efficient cows). For the final GWAS, the FULL dataset with ranked phenotypes was used. Five models were evaluated for each GWAS, including the general linear model (GLM), mixed linear model (MLM), multiple loci mixed model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK). The model that best represented each dataset as determined by quantile-quantile plots was used for downstream analysis. Although results of the GWAS were not significant (Bonferroni threshold), associations were identified on BTA10, 16, 17, 25, 27 and 29. Positional candidate genes in the associated regions include: FOXN3, UPB1, SNX29, DDX54, LOC112444612, RITA1, and TACC1. Further functional analyses are required to confirm these findings; however, this work provides a foundation for identifying genes and gene mutations influencing this newly described phenotype.
209 Prevalence of Antimicrobial Resistance Genes and Mobile Genetic Elements in the Swine Gut Microbiome
Authors: McCullough Taylor M , Farzan Vahab , Surette Michael , Cicek Nazim , Derakhshani Hooman 
Published: November 2023

Abstract
Antimicrobial resistance (AMR) is one of the most pressing threats to public health. It contributes to over a million deaths a year currently and by 2050 it is expected to cause more annual death than cancer. The swine industry has taken important steps to address the AMR crisis by phasing out the use of antimicrobial growth promoters. Nonetheless, the use of antimicrobials for controlling infectious diseases on swine farms remains high, particularly during the nursery stage of pig production. This has raised concerns about the potential role of the swine industry in the emergence and spread of antimicrobial resistance genes (ARGs) capable of conferring resistance to medically important antimicrobials. While traditionally ARGs have been studied in the context of pathogens, there is growing evidence that the natural microbiome of humans and animals can also serve as a significant reservoir of ARGs. Of particular importance is the association of ARGs with different classes of mobile genetic elements (MGEs) which can facilitate the horizontal transfer of genes among commensal bacteria and pathogens. In this study, we evaluated the diversity and distribution of ARGs and their associated MGEs in the swine gut microbiome. To achieve this, we isolated and sequenced the whole genomes of 130 unique bacterial isolates from stool, digesta, and mucosa of healthy adult sows and their piglets. Screening of genomes for the presence of ARGs was performed using the Resistance Gene Identifier (RGI) and Comprehensive Antibiotic Resistance Database (CARD), resulting in the identification of 323 ARGs across 117 genomes. Among these, genes predicted to confer resistance against tetracycline, lincosamide, beta-lactams, and fluoroquinolone were the most prevalent across all genomes. Importantly, we observed that several strictly anaerobic species belonging to gut-specific lineages including Lachnospiraceae, Megasphaeraceae, and Desulfovibrionaceae contained large ARGs pools spanning more than five different classes of antimicrobials. Further, we screened the flanking regions of ARGs for the presence of signature genes of MGEs including recombinases, phage integrases and capsids, and type IV secretion system. A total of 60 ARGs were identified to be associated with different classes of MGEs, including integrative and conjugative elements (ICEs; n = 30), bacteriophages (n = 8), integrative mobile elements (IMEs; n = 6), and plasmids (n = 3). Overall, our study highlights that ARGs, including those conferring resistance to medically important antimicrobials, are prevalent across different lineages of the swine gut microbiota. The association of the identified ARGs with MGEs warrants further in vitro experiments to evaluate the risk of transmission of resistance to zoonotic pathogens capable of infecting humans and animals.
214 Effects of Fiber Concentration and Fermentation Rate on Reproductive Performance, Nutrient Digestibility, and Immune Response of Lactating Sows
Authors: Wang Tao , Langendijk Pieter , Camats Lluís Fabà , Mcknight Leslie L , Pinar Arantxa Asun , Cai Zhen , Yang Chengbo 
Published: November 2023

Abstract
High fiber diets are known to have many benefits to sows (e.g., improving reproductive performance such as vitality of piglets, stimulating gut health, and improving well-being), and due to their fermentation properties, they may have different functions in lactating sows. Fast fermentable fiber favors the growth of beneficial microbiota which contributes to improved gut health, and slow fermentable fiber increases the fecal mass and provides a delayed release of some nutrients which benefits the farrowing process of sows. On the other hand, high fiber diets may reduce feed intake and nutrient digestibility. The objective of this study was to investigate the effects of dietary fiber concentration and fermentation rate on lactating sow performance, nutrient digestibility, and immunity. Four diets were formulated with increasing fast fermentable fiber, with diets 1 and 2 formulated at low (15%) total dietary fiber (TDF) and diets 3 and 4 at high (25%) TDF. The proportion of fast fermentable fiber in total diet of 4 treatments were 1.25%, 2.5%, 3.75%, and 5% respectively. The main fiber sources were sugar beet pulp, oat hull, and barley. Digestible energy, crude protein, and lysine levels were comparable among each treatment group. A total of 136 lactating sows (Landrace × Large White) were blocked by parity, body weight (BW), and back fat (BF), and then randomly assigned to each block (8 blocks). Feed allowance was set to increase from 3 kg/d (primiparous) or 3.5 kg/d (multiparous) at farrowing to a maximum of 7 kg/d or 8 kg/d at 7d or 8d post farrowing. Results showed that sows in high fiber groups had an increased litter weight gain and BF loss (P &lt; 0.05), and sows in fast fiber groups showed a decreased BW and protein loss (P &lt; 0.05). Low fiber fed sows showed a significantly increased digestibility of protein, gross energy (GE), and dry matter compared with high fiber ones (P &lt; 0.05). Sows fed with slow fermentable fiber in the low fiber groups showed greater digestibility of GE, protein, and dry matter compared with the ones fed with fast fermentable fiber; however, the opposite was true in high fiber groups. Fiber concentration and fermentation rate did not show significant effects on serum IL-8, IL-10, TNF-α, or endotoxin of sows (P &gt; 0.05). In conclusion, high fiber diet increased BF loss and negatively influenced nutrient digestibility while having positive effects on litter growth. The negative effects of fiber were partially compensated by increasing the soluble fraction. Based on the current study, when feeding lactating sows a diet with high fiber, a relative increase of fast fermentable fiber is the most favorable feeding strategy.
224 Effects of Feeding Hybrid Rye Grain as a Replacement for Barley Grain on Feed Intake, Ruminal Fermentation, and Site of Nutrient Digestion for Finishing Beef Cattle
Authors: Zhang Fuquan , Brattain Rebecca S , Carey Rachel E , Wehrle Herman , Penner Greg B 
Published: November 2023

Abstract
The objective of this study was to evaluate effects of increasing hybrid rye as a replacement for barley grain on feed intake, ruminal fermentation, and site of nutrient digestion in finishing cattle. Eight ruminally and duodenally cannulated Hereford-cross heifers (starting body weight = 514 ± 25.3 kg) were used in a replicated 4×4 Latin square design with 21-d periods including 15 d of dietary adaptation and 6 d of sample collection. Dietary treatments included a control diet with 10.0% hay, 85.2% barley grain, and 4.8% of a vitamin and mineral supplement on a dry matter (DM) basis. Hybrid rye grain replaced 33, 67, or 100% of the barley grain. Both cereal grains were dry rolled to 80% processing index. Feed, refusals, ruminal fluid, duodenal digesta, and fecal samples were collected. Data were analyzed using the MIXED procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC). Increasing hybrid rye inclusion tended (P = 0.052) to linearly decrease DM intake. Additionally, increasing hybrid rye grain linearly decreased mean and minimum ruminal pH (P &lt; 0.01) and increased the duration (P &lt; 0.01) and area (P = 0.01) that pH was less than 5.5. There was no effect of hybrid rye inclusion on total short chain fatty acid, lactic acid concentrations, or osmolality. Likewise, the molar proportion of acetate and butyrate were not affected by hybrid rye inclusion. Propionate tended to linearly increase with increasing hybrid rye inclusion (P = 0.08). Increasing hybrid rye linearly increased NH3-N concentration (P = 0.03). Ruminal organic matter (OM) digestibility tended to linearly increase (P = 0.08) and ash-free neutral detergent fiber (aNDFom) digestibility linearly increased (P &lt; 0.01) when increasing hybrid rye. There was no effect on ruminal starch digestibility (71.1 ± 5.12%). Intestinal digestibility of CP linearly decreased (P = 0.050), but there were no effects for other nutrients. Increasing hybrid rye linearly increased apparent total-tract DM, OM, and aNDFom digestibility (P &lt; 0.05) but did not affect starch digestibility (97.4 ± 0.42%). Increasing the inclusion rate of hybrid rye grain at the expense of barley grain in finishing diets may decrease DMI and increase risk for ruminal acidosis; however, hybrid rye inclusion did not influence the site or extent of starch digestion and increased total tract digestibility of DM, OM, and aNDFom.
66 Emerging Precision Ranching Technology Is Enabling the Development of a “smart” Biome
Authors: Church John S , Bork Edward 
Published: November 2023

Abstract
Precision ranching technology is revolutionizing remote data collection from livestock and the land base they depend on, greatly improving our ability to assess the entire biome. Remotely Piloted Aircraft System (RPAS or drone) based remote sensing to date has been used primarily to assess intensive cropping; but RPAS systems equipped with interchangeable cameras: high-resolution visual, thermal, LiDAR, and multi/hyperspectral imagers are now being deployed on rangelands, to monitor subtle changes in the visible, near infrared and infrared spectrums (radiation) that both plants and animals reflect. A single RPAS system can now be used simultaneously for high-quality vegetation mapping and behavioral analysis of animals, providing a suite of comprehensive data-collection tools for studying livestock in a variety of landscapes and rugged terrain. For example, we have used RPAS systems to measure behavioral and physiological indicators of cattle heat stress in feedlots and on pasture (Mufford et al., 2021). These same drones can be utilized for RPAS collection of high-resolution imagery (using multi/hyperspectral imagers and LiDAR) for vegetative and topographical mapping, greatly improving our ability to visualize and characterize habitat attributes such as forage availability, quality (stage of growth) and accessibility. Equipping cattle with new tracking technology, including "smart" GPS ear tags, rumen boluses, and wireless fencing collars (based on low-earth orbit satellites and cellular networks) enable animals to be readily identified and tracked on the landscape, while providing invaluable physiological data, such as internal body temperature to monitor estrous, heat stress, or the onset of disease (Figure 1). Additionally, rapid advances in wireless fencing systems have the potential to improve livestock management through autonomous mustering or the implementation of advanced rotational grazing for use in regenerative agriculture efforts. Wireless fencing may decrease production (infrastructure) costs, while also providing a strategy to better align forage demands with use, and thereby enhance pasture condition at the habitat and landscape level. Finally, non-invasive pasture weighing systems, enabled with or without RPAS technologies, are capable of monitoring key livestock production metrics year-round. Together, these technological advances enabled by this new "smart biome" will improve animal health and welfare while ultimately enhancing the sustainability of extensive livestock production systems.
83 Eating and Nutritional Quality of Meats from Water Buffalo Versus Cattle. a Review
Authors: Huerta-Leidenz Nelson O 
Published: November 2023

Abstract
Worldwide, water buffalo [Bubalis bubalis (Buffalo)] is commonly raised as a dual-purpose animal (intentionally for dairy production because their meat quality has been generally perceived as poor). Breeding for milk production, hunting, exhibition, or novelty ownership has been the primary use of Buffalo in United States and Canada. A scientific review was conducted to examine the effect of species (Buffalo vs. cattle) on meat sensory and nutritional quality. Compilation of this type of comparative studies is a necessary exercise to inform all segments of the meat value chain, particularly, final consumers. According to a bibliometric analysis it can be estimated that in the last twenty years the Web of Science database has recorded over 500 publications about Buffalo breeding. Unfortunately, the vast majority of studies comparing quality- or chemical-related trails between these bovid species did not plan adequately in the experimental design to raise or fatten them under the same environmental conditions and (or) made comparisons at a given (fair) endpoint [e.g.., same average age or body weight). Furthermore, most literature reviews on the topic made inferences by making use of observational studies and (or) tabulated findings of different researchers that did not include both species in the same experiment or did not use exclusion criteria to minimize the bias of the interspecific alleged contrasts. This presentation will discuss results from selected controlled experiments reporting quality and nutrient composition of meats from cattle vs. Buffalo. Very few controlled studies could be retrieved on comparison of meat quality (n = 13) and nutrient composition (n = 8) between Buffalo versus indicine (Bos indicus) or European (Bos taurus) cattle. Results from four out of thirteen comparative studies reporting sensory and (or) textural quality traits favored beef; however, three of these experiments only considered textural variables; one of them only included 16 animals older than 50 months of age whereas in the second companion study one half of the experimental group (n = 8) consisted on animals aged 48 to 54 months. According to the survey on proximal/nutrient composition there are minor differences between meats from both species. The results presented herein reveal the potential of young buffaloes to produce comparable or higher-quality meat than cattle counterparts, even under free-range conditions.
81 Meat Options for Dinner: the Road Less Travelled (Bison edition)
Authors: Galbraith Jayson 
Published: November 2023

Abstract
Consumers expect selection in almost every category of purchase including protein from meat sources. There are a variety of meats consumed worldwide with sustained marketing efforts for many species. This presentation will serve as an introduction to the topic of meat proteins from novel species, consumption trends and importance of understanding characteristics of specific meats. Bison, goat, ostrich, elk, deer, yak, water buffalo, horse, donkey, rabbit, wild boar, deer, alligator and llama are all consumed in various quantities in different parts of the world. Understanding reasons for meat selection and the many factors that can impact meat quality can help align production and marketing decisions for optimal consumer satisfaction. Animal genetics, feed, pre-slaughter handling and transport, proper stunning, carcass chilling, cold chain continuity and preparation of the meat can all influence the end eating experience. Research into meat characteristics of various species supports marketing efforts and puts integrity on nutritional claims. An example of this is bison meat marketing which promotes a lean, healthy meat raised on sustainable production systems in Canada and the USA with a rich history behind it. Nutritional analysis of bison meat and production research helps support these claims. Investigation into characteristics of meat from several species throughout the world could broaden opportunities for successfully marketing them as niche products.
228 Food for Thought: How Influenceable Is the Next Generation Consumer
Authors: Hiltbrand Karen A , Corbitt Katie , Coursen Madison , Martin David , Mullenix Kimberly , Ross Derek , Youngblood Ed , Smith Brandon B , Mulvaney Donald 
Published: November 2023

Abstract
Spread of misinformation and disinformation in animal agriculture is rampant in social media and then add the theory of social contagion, and the reach of this information and its impact on social licensure becomes extensive. A research study evaluated susceptibility of young consumers to be affected by false information pertaining to the beef industry found in segments of YouTube videos as well as their level of pre-study food industry knowledge as determined by a Food Familiarity Index (FFI) score. This mixed-methods study included a total of 15 next generation consumers who viewed two different YouTube video clips about agriculture, one being categorized as misinformation and one communicating accurate, research-based information. Level of trust among participants was then gauged using the continuous response measurement (CRM) instrument to identify critical moments of trust and distrust which can be found in the included figures as well as to then to craft participant narrative about perceptions of the beef industry enabled by responses from the focus group. It was found that those who have less knowledge about the food industry are much more vulnerable (P &lt; 0.05) to being misinformed and are more apt (P &lt; 0.05) to be influenced by misinformation Figure 1 and 2). Through engagement in thought-provoking discussion and analysis of what may have encouraged higher or lower levels of trust among the participants, this study contributes to a body of literature that may help communicators within animal agriculture to better understand positions and ability to share information about the agriculture industry to American consumers.
230 Opportunities for and Threats Against Animal Production in the Commonwealth of Pennsylvania: the Need for Animal Scientists to Have a Role in Informing Society
Authors: Gambino Chris , Buzzeo Maddie 
Published: November 2023

Abstract
Animal agriculture is critical to the economy and livelihoods in the Commonwealth of Pennsylvania. Animal agriculture is directly impacted by feed production, weather, disease pressure, regulations, and trade. Few of these, if any, are easily predictable. Thus, thirty-five diverse stakeholders across the supply chain, including feed mills, producers, veterinarians, animal scientists, and policymakers, came together with twenty undergraduate students to scan how factors like political, economic, social, and technological issues impacted the current and future state of animal production in the Commonwealth. Stakeholders were grouped by sector resulting in seven groups (e.g., production, feed processors, meat processors, animal health, conservation, policy, and finance). Session One asked participants to answer, ‘How will the changing outside world affect animal agriculture in the Commonwealth?’ While Session Two asked participants to answer, ‘Does the Commonwealth have the people, practices, equipment, etc. to fight threats and seize opportunities?’ All groups reported their discussions of opportunities and threats. These points were captured and then coded by issue type (e.g., political or social). Across all groups (i.e., 100% of groups), the lack of agriculture literacy in the consumer base was identified as a major threat to animal production in the Commonwealth. Three of seven groups (43%) recognized the political and financial momentum for climate-smart agricultural research and practices as an opportunity for academia, industry, and farmer partnerships. Additionally, three of seven groups (43%) saw increasing markets and decreasing costs of alternative, cultured proteins as a threat to animal production. Groups were split on whether new agriculture technologies were an opportunity or a threat. Some saw new technologies as a threat given the aging farmer population in the Commonwealth, while others saw new technology as an opportunity for better resource use and combating labor shortages. Albeit being state-specific, when taken together these findings provide insight into national-level trends in opportunities and threats that the animal sciences can help to seize and combat. These findings highlight the importance of animal science exiting the benchtop, the farm, and the classroom to better engage consumers and decision-makers seeking information about animal agriculture.