bluuebunny/crossref_metadata_2025_split huggingface dataset:
128 Reviewing the Definition of Mortality in Broiler Chickens
Authors: Richter Jennifer , Bussiman Fernando , Hidalgo Jorge A , Breen Vivian , Misztal Ignacy , Lourenco Daniela 
Published: November 2023

Abstract
Mortality has been a trait of importance in livestock species, especially for poultry, as birds continue to become more efficient and grow larger, and mortality rates have shown an increase at the phenotypic level. Mortality at different stages may be due to different genetic, environmental, and biological factors; however, in most cases, selection can be based on overall mortality. This study aimed to investigate alternative models and trait definitions of mortality by exploring the classification of mortality into different life stages and including a maternal effect in the model. Data provided by Cobb-Vantress, Inc. included mortality records from three separate lines of chicken making up about three generations worth of data. The datasets included records for mortality (0-1) and weekly mortality (0-10) recorded on individuals during their first ten weeks of life. Due to low incidence levels of weeks seven through ten for weekly mortality, those birds were combined with those that survived the first six weeks. Three models with different trait definitions were considered in this study. They were compared against a benchmark model with overall survival as trait definition (M0). Each line was evaluated separately for each model investigated, and the traits under different definitions were treated as binary traits. Thus, threshold models were used to estimate variance components under a Bayesian approach via the Gibbs sampling algorithm implemented in Gibbsf90+ software. The first model and trait definition (M1) investigated was a single trait model with weekly mortality classified into a binary response to whether the bird died within the first six weeks of life (BMORT). The second model and trait definition (M2) investigated was a bivariate model that classified weekly mortality into early (EMORT; weeks 1 to 3) and late (LMORT; weeks 4 to 6) mortality. The heritabilities ranged from 0.11 to 0.19 for M1, 0.10 to 0.21 for EMORT, and 0.15 to 0.17 for LMORT. For both models investigated, heritabilities were greater than that of M0, ranging from 0.03 to 0.09. The second model was additionally run with the maternal effect (M3) composed of the additive maternal and maternal permanent environmental (mpe) effects to investigate any potential effect on the estimated variance components. The maternal heritability and the percentage of phenotypic variance explained by mpe ranged from 0.02 to 0.03 and 0.01 to 0.04, respectively. Including the maternal effect considerably decreased direct heritability for EMORT but not for LMORT, indicating the maternal effect plays an important role in early mortality. The genetic correlations between EMORT and LMORT were low, ranging from 0.23 to 0.44; therefore, it may be necessary to include both traits in the selection index to make better-informed decisions. Selecting against early and late mortality may help improve overall livability in broiler chickens.
125 Implementing a Genetic Evaluation Program for Acute Hepatopancreatic Necrosis Disease Resistance in Penaeus Vannamei (Pacific White Shrimp)
Authors: Ampofo Issabelle , Mai Hung , Dhar Arun , Greevers Daniel , Wright Harris , Fragomeni Breno O 
Published: November 2023

Abstract
This study aims to evaluate the feasibility of a genomic evaluation program for Acute hepatopancreatic necrosis disease (AHPND) resistance in a commercial population of Penaeus vannamei. AHPND is caused by a strain of Vibrio parahaemolyticus (VpAHPND) producing a binary toxin. It is a World Organization for Animal Health (WOAH, Paris, France)-listed bacterial disease that has caused severe economic losses to the shrimp industry worldwide in recent years. The working hypothesis of this study is that the genetic variation in a commercial P. vannamei population allows an efficient genetic and genomic selection program. To investigate the genetic parameters for AHPND resistance, a controlled challenge experiment was performed at the Shrimp Improvement System biosafety laboratory in Miami, Florida, following an immersion challenge protocol using 4.95 × 107 CFU/ mL bacteria and Specific Pathogen Free (SPF) P. vannamei post larvae (n = 2,400) representing 40 selected families. The bioassay was terminated at 3 days post-challenge. Each family consisted of 60 animals, with one-half of the families (n = 20) representing a fast-growth (FG) line and the remaining one-half (n = 20) representing a slow-growth (SG) line. Survival was recorded as a binary of dead or alive at the end of the three days challenge experiment. Variance components were estimated under an animal threshold binary model using a Gibbs sampler. Estimation of genetic parameters was done within lines and by combining all data records. The average hazard risk ratio (HRR) of survival was 80% greater for the FG line (average mortality 40%) than the SG line (average mortality 20%, P &lt; 0.05) based on survival analysis with a 31% mortality rate combining all data records. The posterior mean estimates of heritabilities were 0.14 (± 0.06) for FG, 0.16 (± 0.07) for SG, and 0.38 (± 0.08), combining all records. Estimated breeding values (EBVs) based on the animal threshold binary model ranged from -0.76 to 1.01 on the liability scale. Spearmans’ rank correlation coefficient between the average EBV of parents and the average mortality rates of corresponding families was 0.98. The results suggest that a breeding program for AHPND resistance is feasible. Moreover, the heritabilities suggest that both lines will respond to mass selection due to the presence of additive genetic variation for APHND-survivability. The next step of this project is to genotype animals from every family and implement a genomic selection program. Additionally, high throughput laboratory results and histopathology scores will be introduced in the genetic evaluation as correlated traits.
138 Sire Differences for Blood Urea Nitrogen (BUN) in Hereford Cattle
Authors: Hurst Caleb W , Enns R Mark , Huffhines Craig , Stackhouse-Lawson Kim R , Speidel Scott E 
Published: November 2023

Abstract
Excess Nitrogen excretion is a growing concern worldwide within animal agriculture, and blood urea nitrogen (BUN; mg/dL) is known as a predictor of nitrogen excretion in cattle. The objective of this study was to determine sire differences in BUN within a population of Hereford steers. Steers (n = 74) were born between March and June of 2021 from a reference sire herd for The American Hereford Association in Western Nebraska. Sixteen different Hereford sires from The American Hereford Association reference sire program produced offspring used in this study. The steers entered an on-site feed intake unit and were fed a finishing diet consisting predominantly of corn, corn distiller grain, and corn silage. Animals were subjected to a 21-d warm-up period with a 55-d individual feed intake test period. Blood samples were collected on day 43 of the test period. Blood samples were then centrifuged to extract serum. The Urea Nitrogen (BUN) Colorimetric Detection Kit by Invitrogen was used for the assay. The average BUN concentration for all animals in this study was (0.492 ± 0.061 mg/dL). A generalized linear regression model was used to determine sire differences in BUN concentrations. Factors considered were sire and pen group. The sire with lowest least squared mean progeny BUN concentration estimate was (0.0362 ± 0.08 mg/dL; n = 4), and the highest was (0.605 ± 0.03 mg/dL; n = 7). Sire differences (P &lt; 0.05; r2 = 0.36) were found to be important sources of variation as evidenced by its r2; however, pen group (P = 0.65; r2 &lt; 0.05) appeared to have little impact on variation. The differences in sires indicate genetic differences could be leveraged to reduce excess nitrogen excretion in cattle populations.
145 The Relationship of Methane Emissions with Stayability in Angus Cattle
Authors: Torres-Quijada Isaac F , Speidel Scott E , Zuvich Miranda L , Raynor Edward J , Carvalho Pedro H V , Place Sara E , Stackhouse-Lawson Kim R , Enns R Mark 
Published: November 2023

Abstract
The dairy and beef industries have been identified as an important producer of methane emissions, yet little is known of its relationship to other economically relevant traits. Stayability (STAY) is a fertility and longevity-related trait with EPD (Expected Progeny Differences) representing predicted genetic differences in the probability of daughters remaining in the breeding herd until six years of age. Understanding the relationship between methane emissions and STAY might inform breeders of the consequences of selection on either trait. The objective of this study was to determine the relationship of methane emissions with STAY in Angus cattle (Bos Taurus) from Colorado State University’s John E. Rouse Beef Improvement Center located in southern Wyoming. A total of 123 animals (86 steers, 37 heifers) were sorted into four different pens where individual methane emissions were measured using a GreenFeed system (C-Lock, Rapid City, South Dakota). Stayability was evaluated using EPD values. A general linear model was used to calculate the regression of the average methane emission of each animal measured in grams/day (mean = 163.08, SD = 38.75, min = 87.72, max = 247.03) on STAY (mean = 0.59, SD = 0.69, min = -2.41, max = 2.36), including age in days (mean = 258.2, SD = 20.01, min = 200, max = 298) and pen as effects in the model. The regression of methane emission on STAY EPD was 0.52, however, it was not significant (P = 0.87). The effect of pen was significant (P &lt; 0.001?). Age was significant, having an effect of 0.6794 (P = 3.93e-08). This suggests that younger individuals had decreased methane emissions. These preliminary results indicate that there is no significant relationship between methane emissions and STAY EPD.
140 Targhee Sire Benchmarking at the U.S. Sheep Experiment Station
Authors: Wilson Carrie S , Taylor J Bret B , Murphy Tom W , Stewart Whit C , Notter David R , Lewis Ronald M 
Published: November 2023

Abstract
The Targhee breed was developed at the U.S. Sheep Experiment Station (USSES) starting in 1926, and has become an established range breed used commercially in the Western U.S. Our objective was to benchmark the performance of industry-based (external) Targhee sires with those currently in use at USSES. Nineteen Targhee sires from 12 flocks were incorporated into the USSES breeding flock starting with the 2015 breeding season. Data were measured through 2022 for 3 production and 12 wool traits with a range of 180 to 1,967 records per trait. Externally sourced sires averaged 38.3 progeny (7 to 78), with 0 to 4 ram lambs (15 total) and 0 to 15 (106 total) ewe lambs retained per sire in the flock. They were ancestors of 984 grand-progeny. USSES sires averaged 25.0 progeny (5 to 52), with 0 to 1 ram lambs (2 total) and 0 to 8 (53 total) ewe lambs retained per sire. They had 275 grand-progeny. Pedigree data was used to compute the marginal genetic contributions for each sire to the current flock using ENDOG. External sires had a cumulative contribution of 31.9 percent (0.4 to 3.9) while the USSES sires contributed 1.4 percent (0.0 to 0.9). Using R, fixed effects examined were age of dam, lamb sex, lamb birth year, grazing group, and type of birth/rearing. Significant variation explained in a trait by main effects (P &lt; 0.005), and their two-way interactions (P &lt; 0.001), were included in the final linear mixed models fitted. Externally sourced and USSES sires were assigned to separate genetic groups to account for the anticipated differences in genetic base. Using WOMBAT, a univariate animal model was fitted to estimate variance components and predict estimated breeding values for each lamb trait. Selection of random effects was based on log-likelihood ratio tests. Final models fitted and estimated heritabilities are summarized in Table 1. Total litter weight at 120 days per ewe lambing (TW120) was evaluated using a repeated measures model with direct additive and permanent environmental random effects of the ewe. Genetic group solutions were not significantly different (P &gt; 0.05) for any traits evaluated. Since both sire groups originated from the same population, this suggests significant selection divergence had not occurred between industry and USSES flocks. Incorporation of external Targhee sires increased the genetic diversity of the USSES flock. It also strengthened industry ties to the USSES flock, which will benefit the commercial genetic evaluation conducted by the National Sheep Improvement Program. USDA is an equal opportunity provider and employer.
160 Effect of Diets Containing Soybean Co-Products Formulated for High-Risk Stocker Cattle on Growth Performance, Morbidity and Mortality Associated with Respiratory Disease
Authors: Midkiff Kirsten A , Kegley Beth B , Cheek Robin A , Galloway Doug L , Reynolds Jana L , Shoulders Benjamin P , Powell Jeremy G 
Published: November 2023

Abstract
The objectives of this study were to determine the effect of including soybean co-products on growth performance and respiratory disease incidence in high-risk stocker cattle. For this study, crossbred beef bulls and steers [n = 272; initial body weight (BW) 230.9 ± 19.7 kg] were purchased from local auction markets at 3 time points (load 1: n = 93 cattle; load 2: n = 91 cattle; load 3: n = 88 cattle). On day 0, cattle were processed (ear tagged, vaccinated, dewormed, ear notched for identification of cattle persistently infected with bovine viral diarrhea virus, castrated intact bulls), stratified by BW and allocated randomly to 1 of 8 pens (0.45 ha). Pens were assigned randomly to 1 of 3 dietary treatments: 1) a control supplement containing no soy co-products (CON); 2) a supplement containing soybean meal (SBM); or 3) a supplement containing soy oil (SBO). All supplements were isonitrogenous and isoenergetic. Cattle were fed supplements (2.45 kg DM/day) and offered bermudagrass hay for ad libitum intake for a 42-day trial. Body weights were taken on days 14, 28, 41, and 42 of the trial. Each morning, cattle were observed for signs of morbidity. If presenting with symptoms, cattle were pulled and rectal temperatures were recorded; if temperature exceeded 40°C, calves were treated according to a standard protocol. Cattle were deemed chronic if they received 3 antibiotic treatments and had an overall average daily gain (ADG) of less than 0.5 kg/d. Statistical analyses were performed using SAS 9.4, with PROC MIXED used for BW, ADG, and antibiotic cost analysis. Body weights were analyzed with the repeated measure of day and for treatment, day, and treatment by day interaction. PROC GLIMMIX was used for morbidity and mortality analyses. There was no treatment by day interaction (P = 0.99) or main effect of treatment (P = 0.86), but there was a day effect (P &lt; 0.0001) with BW increasing throughout the trial. Average daily gain was not affected by treatment (P ≥ 0.42; 0.81 kg/d for SBM, 0.79 kg/d for SBO, and 0.76 kg/day for CON). Overall morbidity and mortality were 71% and 1%, respectively, and were not affected by treatment (P = 0.62 and P = 0.99, respectively). Relapse rates and chronics were not affected by treatment (P = 0.52 and P = 0.51, respectively). Total cost of antibiotic treatments was not different (P = 0.8; $30.37 for SBO, $28.95 for CON, and $28.52 for SBM). While the inclusion of soybean co-products did not affect BW, respiratory disease incidence, or cost of antibiotic treatments in high-risk stocker cattle, further work will focus on haptoglobin, hemocytology, and antibody titer responses during the receiving period.
59 A Student Perspective on the Importance of Inclusive Pedagogy
Authors: Tillquist Nicole M 
Published: November 2023

Abstract
Diversity, equity, and inclusion (DEI) in higher education is critical for success of all students including those with marginalized identities. Implementing an inclusive pedagogy involves consideration of all student experiences, backgrounds, and identities. Students who identify within the lesbian, gay, bisexual, transgender, queer plus (LGBTQ+) community can benefit from a more inclusive learning environment. Within the classroom setting and individual courses in particular, including pronouns on course syllabi, using non-binary language, and asking for/respecting preferred names are all examples of simple changes that can be made to create a safe space for LGBTQ+ students. Faculty can also demonstrate a commitment to inclusion outside of the classroom by including pronouns in email signatures or by having DEI training stickers on office doors. These efforts can indicate that faculty are striving to provide a safe space where students can be themselves and that they are committed to being supportive educators that students can trust. Exploring the student perspective offers a unique opportunity to identify potential omissions or oversights in existing curricular and larger systemic factors that can contribute to a lack of inclusion, and to consider potential strategies to ensure promotion of LGBTQ+ inclusive approaches for students in higher education.
4 Hands-On I: Building an Agent-Based Model in Anylogic
Authors: McDonald Wade 
Published: November 2023

Abstract
Livestock farming systems (LFS) have detrimental effects on the environment, associated mainly with feed production, enteric methane and emissions from manure. LFS are complex because they are structured by multiple interactions between biological and human-controlled processes, at various organizational levels. Their behavior and the extent to which feeding strategies can mitigate this environmental burden is not always easily predictable. Dynamic mechanistic models of LFS can simulate the effects of feeding strategies on both animal performance and the associated excretion of nutrients. These models are useful tools to produce the life cycle inventories needed in the second step of a life cycle assessment. In the pig-fattening unit, the effects of multiphase group feeding depend largely on the variability of growth potential among pigs and the farmer has decisions that can target either the group of pigs or each individual (e.g., when choosing pigs to deliver to slaughterhouse). Therefore, simulating the growth trajectory of each individual pig and events like deliveries to slaughterhouse makes it possible to estimate the response of the pig population rather than the average pig to feeding strategies. Individual-based models (IBM) are particularly adequate because they make it possible to simulate each individual and to build the response of the population from the aggregation of individuals. Agent-based models are IBM that rely on self-governing agents made of properties, behavioral rules and resources that allow each agent to make decisions upon the occurrence of an event, which can be triggered randomly or not. This hands-on will focus on a specific example dedicated to the simulation of the response (growth, nitrogen excretion and subsequent gaseous emissions from manure) of a population of fattening pigs to a multiphase feeding strategy. In a first step, we will develop a simplified individual-based model of a pig-fattening pen including pigs and the farmer as agents. In a second step, we will improve this model by introducing interactions between these agents. For both steps, we will work with python language using pre-developed jupyter notebooks.
171 Supplementing Ca Salts of Soybean Oil Via Low-Moisture Molasses-Based Blocks to Improve Reproductive Performance and Overall Productivity of Beef Cows
Authors: Pickett Autumn , Cooke Reinaldo F , Gonçalves Lucas , Burato Samir , Holton Mark , Dias Nicholas Wege , Pancini Stefania , Redifer Tracey , Clark-Deener Sherrie , Currin John , Stewart Jamie L , Fontes Pedro L P , Mercadante Vitor R G 
Published: November 2023

Abstract
This experiment evaluated reproductive and productive responses of beef cows receiving self-fed low-moisture blocks (LMB) enriched or not with Ca salts of soybean oil (CSSO) throughout the breeding season. Non-pregnant, suckling multiparous Angus-influenced cows (n = 554) were assigned to a fixed-time artificial insemination (AI) protocol (day -10 to 0) followed by natural service (day 15 to 70). Cows were managed in 12 groups (46 ± 4 cows/group) maintained in individual pastures, and groups received LMB enriched with 25% (as-fed basis) of CSSO or ground corn (CON) from day -10 to 100. Both treatments were designed to yield a daily LMB intake of 0.454 kg/cow (as-fed basis). Groups were enrolled in an estrus-synchronization + fixed-time AI protocol from day -10 to 0 (AI occurred on day 0) of the experiment and beginning 15 days after AI cows were exposed to mature Angus bulls for 55 d. Pregnancy status was verified on day 55 and 100 of the experiment, and cows that gave birth during the initial two weeks were considered pregnant to fixed-time AI. Calf birthdate and weight was recorded during the subsequent breeding season. All calves were weaned at the same time, and a calf BW and age were recorded. Blood samples were also collected from a subsample of cows on days -10, 0 (fixed-time AI), and 55 (pregnancy diagnosis). All data were analyzed using group as the experimental unit and Satterthwaite approximation to determine the denominator df for the tests of fixed effects. Quantitative data were analyzed with the MIXED procedure of SAS, and binary data analyzed with the GLIMMIX procedure of SAS with a binomial distribution and logit link function. Data were analyzed with group (treatment × location), cow(group), and location as random variables. Significance was set at P ≤ 0.05 and tendencies were determined if P &gt; 0.05 and ≤ 0.10. Cows receiving CSSO had greater (P &lt; 0.01) mean concentrations of ω-6 fatty acids in plasma samples collected on days 0 and 55. Cows receiving CSSO had greater (P = 0.05) pregnancy rate to fixed-time AI (67.2 vs. 59.3%), whereas final pregnancy rate did not differ (P = 0.92) between treatments. Pregnancy loss was less (P = 0.03) in CSSO cows (4.50 vs. 9.04%), which also calved earlier during the calving season (treatment × week; P = 0.04). Weaning rate tended to be greater (P = 0.09) in CSSO (84.8 vs. 79.4%), although calf weaning age and weight did not differ (P ≥ 0.72) between treatments. Kilos of calf weaned/cow exposed was greater (P = 0.04) in CSSO cows (234 vs. 215 kg). Therefore, supplementing CSSO to beef cows via LMB during the breeding season improved their reproductive and overall productivity during a cow-calf cycle.