bluuebunny/crossref_metadata_2025_split huggingface dataset:
183 Ramped Piglet Housing During the Nursery Phase Increases Speed of Loading During Transportation to Market
Authors: Kasakamu Mary L , Young Jennifer M , Samuel Ryan S , Wagner Sarah A , Byrd Christopher J 
Published: October 2023

Abstract
Transportation is an essential component of commercial swine production in the United States. However, the process of transportation, including loading and unloading onto trailers, is a stressful experience for market hogs that results in poor welfare outcomes and substantial economic losses. Therefore, strategies intended to improve the transportation process should be developed. The objective of this study was to determine whether early-life exposure to a ramp structure during the nursery period would affect the ease of loading onto a standard swine trailer at the time of marketing. Weaned pigs (n = 560; 17 to 21 d of age) were penned in groups of 26 and randomly assigned to 1 of 2 treatment groups: 1) RAMP (housed in a standard commercial grow-finish pen furnished with a ramp and platform), or 2) CONTROL (standard commercial grow-finish pen with no ramp and platform). After 6 weeks, the ramps and platforms were removed from the RAMP pens and all pigs were housed under normal commercial conditions until they were marketed over 6 loadout days. After pigs in the barn began reaching market weight at approximately 5 months of age, pigs were moved by treatment in groups of 4 and loaded onto a pot belly livestock trailer (trailer and trucker were the same each time). Additionally, the person moving the pigs up the ramp was the same for all loading dates. The total amount of time it took for each group to navigate the ramp leading to the trailer was determined. Data were analyzed using the mixed procedure of SAS (v. 9.4) with total ramp navigation time as the dependent variable. Fixed effects included treatment, day of loading, and their interaction. A repeated measures statement with pen as the subject was included in the model to account for pen as the experimental unit. Overall, RAMP groups required less time to navigate the ramp onto the trailer than the CONTROL groups (69.12 ± 5.39 s vs. 95.11 ± 5.27 s; P = 0.002). Day of loading also affected ramp navigation time (P = 0.004). Specifically, navigation time on day 1 was greater than all remaining loading days (P &lt; 0.05). Additionally, navigation time on day 2 was greater than day 6 (P = 0.02). No interaction between treatment and day of loading was observed (P = 0.41). In conclusion, exposing pigs to ramp structures within their pens during the nursery phase of production improves the loading speed at market weight by removing novelty associated with the loading ramp. Future research on this topic should incorporate additional behavioral and physiological measures to determine whether exposure of nursery pigs to ramps lowers stress and reduces the likelihood of injury during the transportation process at market weight.
184 Genetic Parameters for Human-Directed Behavior and Intraspecific Social Aggression Traits in Growing Pigs
Authors: Calderon Diaz Julia A , Desire Suzanne , Lewis Craig , Roehe Rainer , Turner Simon Turner 
Published: October 2023

Abstract
This study aimed to estimate heritabilities and genetic and phenotypic correlations for human-directed behavior and intraspecific social aggression traits in growing pigs, and to explore genetic and phenotypic correlations among them. Pigs (n = 2,314) were mixed into groups of 18 animals at 69 ± 5.2 d of age and skin lesions (SL) were counted 24 h (SL24h) and 5 weeks (SL5WK) post-mixing. Individual behavioral responses to isolation in a weighing crate (CRATE, 1 = pig performing exploratory behavior to 4 = pig performing serious, persistent attempts to escape) or when alone in an arena while a human directly approached them (IHAT) were assessed within 48 h post-mixing. During the IHAT, three separate scores were given for each pig based on the severity (0 = none to 3 = severe reaction) of their movement, vocalizations, and vigilance. Additionally, pigs were tested for behavioral responses to the presence of a single human observer walking in their home pen in a circular motion (WTP) within 1 and 4 weeks post-mixing recording pigs that followed, nosed or bit the observer. An animal model was used to estimate genetic parameters for all studied traits using the DMU software. Heritabilities (h2) for SL, CRATE and IHAT responses were low to moderate (0.17 to 0.29), with the greatest h2 estimated for speed of moving away from the approaching observer in the IHAT. Low but significant h2 were estimated for nosing (0.09) and biting (0.11) the observer at 4 weeks post-mixing in the WTP test. Positive high genetic correlations (rg) were observed between CRATE and IHAT responses (0.55 to 0.90), and within SL traits (0.60 to 0.94) while positive low to high rg were estimated within the WTP test (0.24 to 0.59) traits. Positive moderate rg were observed between CRATE and central and posterior SL24h. Genetic correlations between CRATE and IHAT test responses and WTP test traits were low, mostly negative (-0.21 to 0.05) and not significant. Low positive rg (0.06 to 0.24) were observed between SL and the WTP test traits except for the lack of rg between posterior SL24h and pigs biting or following the observer during both tests. Phenotypic correlations between CRATE and IHAT responses and SL or WTP test traits were mostly low and not significant. Under the conditions of this study, h2 estimates for all studied traits suggest they could be suitable as a method of phenotyping aggression and fear and/or boldness in pigs for genetic selection purposes. Additionally, there was evidence of genetic associations between aggression and fear indicators. These findings suggest applying selection pressure to reduce the accumulation of lesions is likely to make pigs more relaxed in a crate environment, but to alter the engagement with humans in other contexts that depends on the location of the lesions under selection.
185 Effect of ad Libitum Versus Limit-Feeding Program at Receiving on Morbidity and Performance of Feedlot Calves
Authors: Funk Rebecca A , Troyer Braden C , Norman Mitchell M , McPhillips Levi J , Erickson Galen E 
Published: October 2023

Abstract
Despite advancements in both vaccine technology and antibiotic therapy, bovine respiratory disease complex (BRD) remains the primary health challenge for cattle feeding operations in the United States. The strategy of limit-feeding calves during the early receiving period (first 28 days) has been proposed as a method to mitigate BRD risk, but limited data are available despite this strategy becoming more common. The objective of this study was to evaluate limit-feeding as a receiving protocol to determine impact on pull rates, receiving performance, and subsequent (Post-receiving) finishing performance. Steers (initial BW = 262 kg; n = 704) were blocked by arrival day (7 blocks) and housed in 44 open-lot pens. Pens were assigned to either limit-fed at approximately 75% of ad libitum or fed ad libitum for the 28-day receiving period. A subset of 216 steers in 14 pens was followed through finishing to evaluate carry-over effects in the finish period (192 days). Dry matter intake (DMI; P &lt; 0.01), average daily gain (ADG; P &lt; 0.01) and ending body weight (P &lt; 0.01) were less for the limit-fed treatment compared with ad libitum due to the limitation of intakes as designed. Intake averaged 70.1% for limit-fed versus ad libitum whereas ADG was 72.6% for limit-fed compared with ad libitum. Because both DMI and ADG were decreased by similar amounts, G:F was not affected (P = 0.28). Numerically better G:F was observed for limit-fed cattle versus ad libitum but this 3.4% difference was not significant (P = 0.28). Morbidity rates for BRD were not statistically different, with ad libitum morbidity of 16.3% compared with 14.3% for limit-fed steers (P = 0.58) Low mortality for the receiving period was observed with 0.84% (3 steers) on limit-fed treatment, and 0% for the ad libitum treatment. For the subset of pens that were followed through finishing, there were no differences (P &gt; 0.18) in ADG or DMI. While not statistically different, there was a 2.2% increase in ADG for steers that were limit-fed during the receiving period, which allowed for similar HCW and final BW (P = 0.39) at slaughter. Other carcass characteristics were also similar (P &gt; 0.74) between steers received with an ad libitum or limit-fed program. No statistical difference (P = 0.29) in the rate of liver abscess occurrence was noted. In conclusion, there was no statistical difference between treatments in early-period morbidity or finishing performance between ad libitum and limit-fed receiving management.
186 Examining the Vaginal Microbiome During Gilt Reproductive Development
Authors: Fowler Emily , Dierking Shannon L , Levesque Crystal L , St-Pierre Benoit 
Published: October 2023

Abstract
Gilt reproductive failure is a common challenge in the US swine industry. Indeed, as many as three million breeding females are removed from swine herds each year, resulting in an annual replacement rate of 40%. Furthermore, about 20% of gilts selected for replacement never successfully enter the reproductive herd. The vaginal microbiome may play a role in gilt reproductive success; this study compared the vaginal bacterial composition from eight gilts at two pre-pubertal time points (d70 and d130 of age). Vaginal swabs were collected and analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from vaginal microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. Seven of the gilts achieved first estrus between d 164 and d 190 days of age based on physical signs of vulva swelling and locked stance in the presence of a boar. One female had no visible signs of estrus before 210 d of age. Beta diversity analysis by PCoA revealed that samples clustered into two separate groups according to time points. Alpha diversity indices (Sobs, Ace and Chao) were numerically decreased between d 70 to d 130. A comparative analysis of the most highly represented Operational Taxonomic Units (OTUs) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified 12 OTUs that varied in abundance (P &lt; 0.05) between the two time points. Notably, OTU SD_Ssd-00001, predicted to be a strain of Lactobacillus amylovorus (99.82% sequence identity), was greatest at d 70 (21.33%), then significantly decreased at d 130 (7.67%). In contrast, OTU SD_Ssd-01393, corresponding to an uncultured species of Prevotellaceae (closest relative: Prevotella disiens, 92.48%), was in less abundance at d 70 (4.87%), but became the most abundant OTU at d 130 (18.19%). The vaginal OTUs identified in this study included not only known bacterial species, such as members of the Lactobacillus genus which have been previously found to be normal and beneficial residents of the human vagina, but also uncharacterized bacterial species. These results are indicative of distinct vaginal microbiome composition between d 70 and d 130 of age and suggest that certain bacterial species could potentially be used as indicators of reproductive potential in gilts.
74 The Dynamic Animal Welfare Concept: A Guideline to Assess, Safeguard and Promote Animal Welfare
Authors: Arndt Saskia S , Goerlich Vivian C , Josef van der Staay F 
Published: October 2023

Abstract
Theoretical concepts are needed to guide and provide the basis for the appropriate assessment, protection and promotion of animal welfare. Due to its multifaceted nature, animal welfare can be approached from different perspectives, depending on ethical assumptions, human interests and culture. In the past, concepts of animal welfare have evolved from the Five Freedoms, which focused on the absence of negative conditions, to Quality of Life and the Five Domains, which emphasized the presence of positive conditions. We build on the existing theoretical framework and present here the Dynamic Animal Welfare Concept (DAWCon, Arndt et al.2022). Based on the adaptive capacity of the individual animal, DAWCon recognizes the dynamic nature of animal welfare and the importance of positive emotional states. We propose that an individual animal is likely to be in a positive welfare state when it is mentally and physically capable and has the ability and opportunity to respond appropriately to sporadic or persistent appetitive and adverse internal and external stimuli, events and conditions. Appropriate responses are elements of a normal behavioral repertoire of the animal. They enable the animal to cope with and adapt to the demands of the (Prevailing) environmental circumstances and to reach a state that it perceives as positive (i.e., that evokes positive emotions). In addition to presenting our conceptual approach, we will outline the issues that need to be considered when assessing welfare, emphasizing that welfare needs to be monitored over time. Animal behavior is highlighted as a key indicator and the role of normal and natural behavior is discussed. To ensure its welfare, an animal must respond and adapt appropriately to the net effects of appetitive and adverse factors. Examples of such internal and external factors and their potential to have sporadic and lasting welfare consequences are discussed. Reference: Arndt SS, Goerlich VC and van der Staay FJ (2022) A dynamic concept of animal welfare: The role of appetitive and adverse internal and external factors and the animal’s ability to adapt to them. Front. Anim. Sci. 3:908513. doi: 10.3389/fanim.2022.908513
17 Nutritional Consequences of Formulating pig Diets with Low Energy Values Using Fibrous Rich Byproducts
Authors: van Dijk Albert , Molist Francesc 
Published: October 2023

Abstract
The objective of this study is to provide insight in how to formulate pig diets in the most economical way in times of high feedstuff prices. Regarding this, energy level and the way of calculating energy in swine feeds will be taking into consideration, as well as the nutrients to energy ratios. Moreover, the effects of diet concentration on feed intake and growth performance of pigs will be evaluated. The lowest cost per energy value in swine feeds can be assessed by iterative simulations in least cost calculations using linear programming. In this case, a fixed nutrient to energy ratio has to be maintained for each cost per energy value that is calculated. Since feedstuff prices are subject to changes, these calculations have to be made on a regular basis. A dataset of 6 growth performance experiments in growing finishing (GF) pigs varying in energy values performed at Schothorst Feed Research (SFR) was analyzed. While decreasing the net energy value of the feed (at fixed nutrient to energy ratios), feed intake and energy conversion increased, while energy intake, daily gain and feed conversion ratio decreased. In general, pigs fed diets with reduced energy concentration are prone to maintain constant daily energy intake by eating more feed until feed intake is limited by other factors, such as physical gut capacity or certain dietary components (Li and Patience, 2017). In the same SFR analysis, the effect of the lysine (and other essential AA) to NE ratio was investigated. While decreasing this ratio, feed intake and energy intake were unaffected, while daily gain decreased, and the feed conversion ratio and energy conversion ratio increased. Another analysis of several GF experiments conducted at SFR was done to assess the optimal amino ccid (SID EAA) content of grower/finisher pig feeds in relation to technical performance, carcass characteristics and profitability. It was concluded that decreasing the SID AA/NE ratio to a certain extend will decrease technical performance (ADG and lean meat %) but increase economical results. However, it must be taken into account that optimal economic performance depends on market situation (feedstuff prices) and production goals (optimal ADG, carcass quality or costs/kg pork). In the current situation with high feedstuff prices, the inclusion of fibrous rich byproducts in the Dutch market may be more economical than corn and soybean meal. For an optimal estimation of the proportion of energy of those fibrous byproducts that will be attributed to the growth and maintenance energy requirements of the pigs, the net energy system is more appropriate than the metabolizable energy (ME) system, because the ME system overestimates the proportion of energy that will be used for growth and maintenance.
100 Pedigree Effective Population Size Affects Genomic Prediction Accuracy in Katahdin Sheep
Authors: Nilson Sara M , Burke Joan M , Lewis Ronald M 
Published: October 2023

Abstract
Katahdin sheep are a composite hair breed of medium-size, relatively prolific, with potential to exhibit resistance to gastrointestinal parasites. Recently, genomic predictions of breeding values were introduced in Katahdins. Prediction accuracy depends on the genetic variation present, and selection using genomically-enhanced breeding values may reduce diversity. We aimed to characterize the current genetic variability in Katahdins utilizing their extensive pedigree. The National Sheep Improvement Program provided the pedigree of 92,030 sheep born from 1984-2019. Two reference populations were defined for animals born between 2017-2019: all Katahdins (n = 23,494), and Katahdins with at least three generations of known Katahdin ancestry (n = 9,327). Using ENDOG and PopReport, effective population sizes (Ne) were estimated. We then considered the effect of Ne on the size of the genomic reference population needed to achieve certain levels of prediction accuracy. Weaning weight, a lowly heritable trait for this breed (h2 = 0.13), was evaluated. Based on individual increase in inbreeding, inbreeding coefficient of animal adjusted for equivalent complete generations, the estimated Ne for the full pedigree, reference 1, and reference 2 were 92, 104, and 87, respectively. When inbreeding coefficients were regressed or log-regressed on birth date and adjusted for generation interval, the Ne estimates were 53 and 49 for reference 1, and 76 and 67 for reference 2, respectively. For our average Ne = 75 with 3,960 effective chromosomal segments, the accuracy of prediction for weaning weight was estimated for genomic reference population sizes (N) of 10k, 15k, 20k, and 25k. Starting at N = 10k, the prediction accuracy was 0.58, and as N increased by 5k increments the accuracy increased to 0.65, 0.70, and 0.74. Conversely, with our smallest Ne = 49 with 2,548 effective chromosomal segments, the prediction accuracy was 0.64, 0.71, 0.75, and 0.78 for N = 10k, 15k, 20k, and 25k, respectively. Estimated Ne varied depending on the method utilized, and tended to be larger for reference 1 than 2. However, this was not the case for Ne based on regression. Inbreeding coefficients were greater in reference 2 than 1, and the generation interval was shorter in reference 2 (2.84 years) than in 1 (2.97 years). These combined differences led to larger Ne estimates for reference 2 than 1, reflecting the impact of different criteria used to obtain this statistic. The generally small, estimated Ne benefitted genomic prediction due to a greater shared number of effective chromosomal segments. Investing in larger genomic reference populations will only marginally increase prediction accuracy even for lowly heritable traits. Selection using genomically-enhanced breeding values will accelerate genetic gains, potentially reducing the Ne of Katahdins and thereby increasing prediction accuracy. Yet, long-term gains may be at risk due to the loss of genetic diversity.
178 Functional Role of Regulatory Elements Informs Complex Trait Variation and Domestication Selection in Farm Animals
Authors: Zhou Huaijun 
Published: October 2023

Abstract
Functional Annotation of Animal Genomes (FAANG) has made significant progress on the improvement of the annotation of the functional elements, particularly non-coding regions in farm animal genomes. Different epigenomes including ChIP-seq for 4 histone marks, ATAC-seq, CTCF-seq, RNA-seq, and Hi-C across different tissues were generated. Thousands of cis-regulatory elements including promoters and enhancers across different tissues in different species were identified and annotated. A comprehensive characterization and comparison of cis-regulatory elements across tissues and species can help us understand the genetic and evolutionary basis of complex phenotypes. We demonstrate that genomic variants associated with complex traits and adaptive evolution in farm animals are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory elements play important roles in domestication processes. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating genome-wide association studies on complex traits, we demonstrate that cis-regulatory elements annotation enhances our interpretations of complex traits variations in farm animals.
57 Concentration of Digestible Energy in Corn-Based Diets Fed to Gestating and Lactating Sows is Increased by Adding Xylanase to the Diets
Authors: Medellin Jessica P Acosta , Espinosa Charmaine D , Ortiz Gemma Gonzalez , Stein Hans H 
Published: October 2023

Abstract
The hypothesis that exogenous xylanase added to diets for gestating and lactating sows will increase the apparent total tract digestibility (ATTD) of gross energy (GE) and total dietary fiber (TDF), and digestible energy (DE) and metabolizable energy (ME) was tested. Two diets for gestating and two diets for lactating sows containing corn, soybean meal, distillers dried grains with solubles, wheat middlings, and soybean hulls were formulated without or with 16,000 BXU per kg of exogenous xylanase (Econase XT; AB Vista, Marlborough, UK). Lactation diets contained an indigestible marker. Diets were fed to gestating and lactating sows in two reproductive cycles. A total of 106 gilts and sows were randomly allotted to the two gestation diets 7 d after breeding in a randomized complete block design with 4 blocks. On d 30 post-breeding, 8 non-pregnant animals were removed. From the remaining 98 animals, 48 sows (24 replicates per treatment, 12 sows per block) were placed in metabolism crates on d 35 (mid-gestation) for 10 d with feces and urine collected for 5 d. The same 48 sows were placed in metabolism crates again on d 95 (late-gestation). All sows were moved to the lactation unit on d 106 and lactation diet feeding was initiated. Fecal samples were collected (grab-sampling) for 5 d starting on d 10 post-farrowing. Sows were weaned on d 20 and 63 sows were rebred. Of these sows, 46 sows were placed in metabolism crates on d 35 and 95 as in the first cycle, and treatments in the farrowing unit were also as in the first cycle. Data were analyzed using the MIXED procedure of SAS with sow as the experimental unit, diet as fixed effect, and block and replicate as random effects. Results indicated that in the first cycle, the ME in mid-gestation, and the ATTD of TDF, and DE and ME in late-gestation were greater (P &lt; 0.05) in sows fed the xylanase-diet compared with the control diet (Table 1). During the first lactation period, sows fed the xylanase-diet had greater (P &lt; 0.05) ATTD of TDF and GE and greater (P &lt; 0.05) DE than sows fed the control diet. During the second gestation period, sows fed the xylanase-diet had greater (P &lt; 0.05) DE and ME in mid- and late-gestation, but no differences were observed in ATTD of TDF (Table 2). During the second lactation period, sows fed the xylanase-diet had greater (P &lt; 0.05) ATTD of TDF and GE and greater (P &lt; 0.05) DE than sows fed the control diet. In conclusion, DE was greater in the xylanase-diet than the control diets during two reproductive cycles, and sows fed lactation diets with xylanase had greater digestibility of fiber.