bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSIII-3 Evaluation of low-cost cow-side tests in developing a selective dry cow therapy program
Authors: Burner Carmen M , Callaway Todd R , Ryman Valerie E 
Published: September 2024

Abstract
Blanket dry cow therapy accounts for approximately one third of antibiotic use on dairies. Selective dry cow therapy (SDCT) is a management strategy that selects quarters or cows to be treated with antibiotics based on herd and/or cow-level criteria. Options for implementing SDCT include both cow-side tests (low-cost, rapid tests and higher cost culture-based SDCT) and historical data (algorithm-based SDCT), or a combination. Considerations made when exploring SDCT options include differences in diagnostic efficacy, cost, etc. The objective of this study is to evaluate the accuracy of common low-cost cow-side tests for diagnosing infection in the development of a SDCT program relative culture-based SCDT. In particular, the California Mastitis Test (CMT) and milk conductivity as measured by Mas-D-Tec were selected given their low input and per cow cost ($17 kit at &lt; $0.10/cow and $400 device with negligible per cow cost, respectively). Late-lactation dairy cows (n = 47) at the University of Georgia Teaching Dairy were enrolled 48 h prior to dry off. On enrollment day, quarter milk samples were aseptically collected, tested utilizing CMT and milk conductivity was recorded. Milk samples were then plated on blood agar, following which, plates were evaluated for microbial growth 48 h later. Quarters were identified as bacteriologically infected or uninfected based on microbial growth. Cow-based SDCT, rather than quarter-based SDCT, was evaluated in this study. Overall, 23.40% of cows were infected at collection. Relative to culture-based selection, the sensitivity and specificity of CMT was 90.9% and 13.9% whereas the sensitivity and specificity conductivity was 81.8% and 27.8%. However, analysis indicated effects seen were not significant (P &gt; 0.05). As a result of CMT and conductivity not yielding a significant effect, a third, yet more costly, cow-side test was evaluated. Selecting cows based on increased milk somatic cell count (SCC) is a central piece in algorithm-based SDCT. Relative to culture-based selection, SCC as a diagnostic indicator was significant (P = 0.01) with a sensitivity of 90.1% and specificity of 55.6%. The accuracy of SCC as a diagnostic tool was 63.8%. Additional data are needed to fully evaluate the applicability of CMT and conductivity as measured by the Mas-D-Tec, especially when considering the perceived economic benefits of implementing SCDT with rapid, low-cost cow-side tests. Utilization of SCC is a viable option given our findings however initial input costs (&gt;$3,000), per cow screening costs ($3 to $12), and labor are all examples of barriers to implementation. In conclusion, the low-cost, rapid cow-side tests assessed in the current study were not effective as diagnostic tools for SDCT. Considering another cow-side test (SCC) may be necessary for producers interested in reducing antibiotic usage and costs. Dairy producers would realize a 45% decrease in dry cow therapy costs and 42% reduction in antibiotic use.
PSIII-15 Feeding patterns of yearling Angus bulls based on feed efficiency metrics
Authors: Katz Amelia R G , Huzzey Julie M , Dubowsky Jason P , McFarlane Zachary D 
Published: September 2024

Abstract
The study objective was to determine how feeding behavior relates to feed efficiency in yearling Angus bulls at the Cal Poly Bull test. Bulls (n = 102) were housed in four pens sorted according to initial body weight (BW; 460 ± 35, 407 ± 15, 374 ± 20, 323 ± 30; mean kg ± SD), resulting in 24 to 28 bulls/pen. Feeding behavior was monitored using an electronic feeding system (SmartFeed, C-Lock, Inc.) during an 85-d feed efficiency test. Four feeders in each pen were filled twice daily at approximately 0630 h and 1700 h. The number of visits to the feed bunk, visit duration, total feeding time, and hourly feed intake were determined from data collected from the feeding system. These data were summarized by hour in a 24-h period, across the 85-d period. Bulls were retrospectively classified into a high feed efficiency group (HIFE) and low feed efficiency group (LOFE) based on an assessment of their summed residual feed intake rank and their feed:gain ratio rank. Within each pen, 5 HIFE and 5 LOFE bulls were selected, resulting in 20 bulls/treatment used for the final analyses. Data were analyzed using the MIXED procedure in SAS 9.4. The model included the fixed effects of feed efficiency group (HIFE vs LOFE), hour (0 to 24), and the feed efficiency group × hour interaction. Bull within pen was considered a random effect and hour a repeated measure. LOFE bulls visited the bunk more frequently throughout the day during the entire testing period (P = 0.04). Differences between feed efficiency groups depended on hour and most differences were observed within 3 h of fresh feed delivery (P ≤ 0.02). A feed efficiency group × hour interaction (P &lt; 0.001) indicated that LOFE bulls had longer feed bunk visit durations predominantly between fresh feed deliveries (P ≤ 0.048). LOFE bulls spent more time feeding throughout the entire day (P = 0.003) when compared with HIFE bulls. Feeding duration per hour was longer for LOFE bulls during the post-morning feeding period (7-h duration) and post-evening feeding period (4-h duration; P ≤ 0.045). More feed was consumed by LOFE bulls throughout the day (P &lt; 0.001), particularly during the post-morning feeding period (P ≤ 0.05). Overall, bulls exhibiting decreased feed efficiency had different feeding behavior patterns in all behavioral categories than their more feed efficient counterparts, especially around feed delivery. Thus, more active bulls at the feed bunk were less feed efficient, and this behavioral pattern may be an important consideration in bull selection.
PSIII-13 Uncovering the genetic basis of cleft palate in Boer goats
Authors: Hoffmann Kenzy , Beever Jonathan E , Rowan Troy N 
Published: September 2024

Abstract
Cleft palate is a genetic deformity that can occur in several species, it is the result of the palate of the mouth not fully forming during gestation. This leaves an opening in the mouth that could extend to the nasal cavity, potentially causing the animal to be unable to eat or drink properly. This typically leads to the breeder euthanizing the animal shortly after birth. The objective of this study was to determine the genetic cause of cleft palate in Boer goats and to develop a diagnostic tool that allows producers to select against it. Blood samples (n = 15) were collected from three Boer goat herds. The samples represented six trios and one quad that included sire, dam, and affected kid(s). All affected kids were sired by the same male. Genomic DNA was extracted and used to generate libraries for whole genome sequencing. An average of 179.7 million reads were generated across all samples (range from 151.2 million to 224.4 million reads) resulting in approximately 10X genome coverage per sample. After sequencing, quality filtering was performed using a nextflow pipeline modeled after the germline short variant discovery best practices workflow from the Genome Analysis Toolkit (GATK) software. After filtering, reads were mapped to the Saanen_v1 reference genome. The pipeline called 18,867,792 variants across the 15 samples. Variants were processed using Ensembl Variant Effect Predictor (VEP) to identify potentially high-impact mutations that may be causal. Additional analyses will be used to refine this list of candidate variants for this condition.
PSV-18 Relationships between serum insulin-like growth factor 1 and cortisol in growing steers to beef production and palatability
Authors: Wesolowski Lauren T , Semanchik Pier L , Simons Jessica L , Carson Chloey P , DiSilvestro Adrianna N , Earnhardt-San Audrey L , Riley David R , Perry George A , Long Charles R , Machado Tanner J , Randel Ronald D , Welsh Thomas H , White-Springer Sarah H 
Published: September 2024

Abstract
Beef cattle breed and temperament are known to impact beef production; however, the physiological pathways linking stress and growth to palatability are not well understood. To test the hypothesis that live animal circulatory cortisol and insulin-like growth factor 1 (IGF1) would be related to temperament, production efficiency, and palatability, Brahman and Angus steers were classified as calm (n = 13 Angus; n = 12 Brahman), intermediate (n = 11 Angus; n = 10 Brahman), or temperamental (n = 12 Angus; n = 12 Brahman) based on their pen score and exit velocity at weaning. Serum samples collected at 10, 13, and 18 mo of age were evaluated for cortisol and IGF1 concentrations. Steers were maintained on grass pasture until they were moved to a feedlot after the 13-mo collection and provided a growing ration. Following the 18-mo collection, steers were sent to a commercial abattoir. Data were analyzed using linear models in SASv9.4 with breed, age, temperament, and all interactions as fixed effects and age as a repeated effect with animal(breed) as the subject. Relationships between variables were assessed with Pearson correlation coefficients. Calm Angus had greater IGF1 than temperamental Angus (P = 0.02) while intermediate Brahman had greater IGF1 than calm or temperamental Brahman (P ≤ 0.02). Temperamental Brahman had greater cortisol concentrations than calm and intermediate Brahman and temperamental Angus (P ≤ 0.01). In Angus, IGF1 concentrations decreased from 10 to 13 mo and from 13 to 18 mo (P ≤ 0.0006). In contrast, Brahman IGF1 concentrations increased with age to be greater at 13 and 18 mo than 10 mo (P ≤ 0.0001). Angus also had greater serum IGF1 than Brahman at 10 mo, but Brahman had greater IGF1 than Angus at 13 and 18 mo (P ≤ 0.0007). In 10 mo Brahman, IGF1 was positively correlated with animal body weight (BW) and average daily gain (P ≤ 0.005). IGF1 in 10 and 13 mo Brahman was also positively correlated with marbling (P ≤ 0.03). IGF1 in 13 mo Angus was positively correlated with Warner-Bratzler shear force (P = 0.02). Cortisol concentrations in Angus were greater at 10 and 13 mo than at 18 mo (P ≤ 0.004) leading to 10 mo Angus having greater cortisol concentrations than Brahman of the same age (P = 0.05). In Angus, at 10, 13, and 18 mo, cortisol was positively correlated with animal BW and hot carcass weight (P ≤ 0.05). At 10 and 13 mo, cortisol was positively correlated with ribeye area in Angus (P ≤ 0.005). These data suggest that serum IGF1 in Brahman is related to growth and lipid metabolism, and tenderness in Angus. However, cortisol concentrations have a more prevalent relationship with Angus growth and subsequently beef production. This project was supported by USDA NIFA Award #2021-67015-33392.
PSV-11 Significance of specialty protein ingredients in feeding programs for broiler chickens on nitrogen utilization and excretion- A meta-analysis
Authors: Njeri Felix M , Ellis Jennifer L , Kiarie Elijah 
Published: September 2024

Abstract
The utility of specialty protein ingredients (SPI) in feeding programs for broiler chickens is premised on poor utilization of conventional vegetable proteins (CVP). The SPI includes ingredients of animal origin such as processed animal proteins (PAP), insect proteins (IP) and further processed conventional vegetable proteins (PCVP) characterized with greater concentration of crude protein/amino acids, and low anti-nutritional factors. The objective of this study was to apply meta-analysis approach of published studies that incorporated SPI to provide insights into their effectiveness on nitrogen utilization and excretion in broiler chickens. The data were retrieved from Web of Science, PubMed, ScienceDirect, hand searching and cross-referencing, and resulted in 44 publications meeting inclusion criteria such as being a broiler study and treatments diets being isocaloric and isonitrogenous Model development was performed in PROC GLIMMIX of SAS and treated the study as a random effect. The SPI protein source (PAP, IP, and PCVP), bird age (starter 0 to 14 d, grower 14 to 24 d and finisher 25 to 42 d), nitrogen intake and level were the main X variables of interest, while outcome (Y) variables explored included nitrogen excretion, nitrogen retention, nitrogen efficiency, average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR). To address heterogeneity in sample size and errors between treatment means from different studies, the WEIGHT statement in PROC GLIMIXX was employed to weight variables using the inverse of their squared variance. The inclusion or rejection of models developed was based on the evaluation of root mean square prediction error and concordance correlation coefficient. Comparatively, the slopes of PAP, IP and PCVP (soybean meal) linearly reduced and quadratically (P &lt; 0.05) increased ADG during the starter phase against their respective controls. The extent ADG was greatest with intake of PCVP followed by PAP. During the grower phase, ADG was highest for PAP, followed by IP with PCVP being the least (P &lt; 0.05). However, PCVP had the greatest ADG during the finisher phase (P &lt; 0.05). On nitrogen excretion, provision of PAP during the stater phase increased the nitrogen excretion while it reduced the excretion during the grower and finisher phase (P &lt; 0.05) relative to control. The intake of IP up to 10% inclusion reduced nitrogen excretion only during the starter and grower phase (P &lt; 0.05) when compared with respective controls. The intake of PCVP reduced nitrogen excretion in all growth stages compared with respective controls (P &lt; 0.05). In conclusion specialty proteins (PAP and PCVP) and insect protein at an inclusion level of &lt; 10%, were effective ways of reducing nitrogen excretion while improving growth performance. Combining these strategies may have a synergistic effect.
PSV-3 Lifetime plasma concentration of select trace minerals in broiler chickens hatched from broiler breeders fed hydroxychloride or organic sources of zinc, copper, and manganese
Authors: Bakhshalinejad Reza , Torrey Stephanie , Kiarie Elijah 
Published: September 2024

Abstract
The objective was to investigate the effects of feeding broiler breeders (BB) hydroxychloride (HC) or organic (OR) sources of zinc (Zn), copper (Cu), and manganese (Mn) from 42 to 63 wk of age (woa) on plasma concentration of trace minerals (TM) in offspring at hatch through to 42 d of life (Table 1 to 4). A total of 408 ♀ Ross 708 and 48 ♂ Yield Plus cockerels were placed in pens (17 ♀ and 2 ♂) and allocated to one of two diets: 1) HO, a blend of 80% HC and 20% OR sources, and 2) OR, 100% OR sources. In total, 2,160 eggs (90 eggs from each pen replicate) were collected and labelled by BB pen at 46, 52 and 62 woa and incubated. Upon hatching, chicks were sexed, weighed, and placed in 24 pens (40 birds/pen) within BB diet identification. For offspring phase, one-half of chicks from BB fed HO or InO were fed HC and the other half were fed inorganic (InO) sources of Zn, Cu and Mn, effectively creating 4 treatments for offspring phase (n = 6; 3 pens per sex). There were no BB diets effects (P &gt; 0.05) on plasma concentration in hatchlings (Table 5, 6). However, BB age effect was such that plasma of hatchlings of 54- and 62-wk-old BB exhibited increased concentrations of Zn, Cu, and Mn compared with those from 46-wk-old parents (P &lt; 0.0001; Table 6-7). Additionally, female hatchings displayed greater Cu concentrations in plasma compared with males (P = 0.024). Broiler chickens fed HC exhibited greater plasma Zn, Cu, and iron on d 21 compared with the other groups (P &lt; 0.05) while 42-d chickens fed HC diet exhibited increased concentrations of Mn and iron compared with the other groups (P &lt; 0.05). Forty-two-d old broiler chickens from 62-wk-old breeders exhibited greater TM concentrations compared with those from younger parents (P &lt; 0.0001). The findings provide valuable insights for enhancing TM supplementation in BB diets to enhance the plasma concentrations of Zn, Cu, and Mn in offspring. Notably, hatchlings fed with HC as a source of Zn, Cu, and Mn exhibited increased concentrations of these minerals through 42 d.
PSV-19 Uncovering breed-origin allele effects and their role in thermotolerance through genome-wide association study in Brangus cattle
Authors: Zayas Gabriel A , Rojas Camila Santos , Hernandez Aakilah , Rodriguez Eduardo E , Beard Ashley , Rafiq Fahad , Davila Kaitlyn Sarlo , Mateescu Raluca 
Published: September 2024

Abstract
In subtropical and tropical environments, beef cattle production faces significant challenges due to heat stress, affecting animal welfare and productivity. To mitigate these effects, producers have turned to crossbreeding and the development of composite breeds like Brangus, which combine the desirable carcass and meat quality traits of European taurine cattle with the thermotolerance of Indicine breeds. However, the genetic underpinnings of thermotolerance in these composite populations are not well understood, owing to the complex nature of measuring related traits and the genetic intricacies arising from crosses of distinct populations. This study aims to identify key quantitative trait loci (QTL) related to thermotolerance, employing an approach that integrates genetic markers alongside the marker’s breed of origin of alleles (BOA) in Brangus heifers. Data were collected on histological sweat gland area (SWA), hair length (HL), and thermal stress slope as a measure of the increase in body temperature from a low to a high temperature-humidity index (TSS), from 2,233 Brangus heifers genotyped with the 250K functional chip. BOA was determined using LAMP-LD software, using Angus and Brahman cattle from the University of Florida’s multibreed Angus-Brahman project as a reference population. We conducted a genome-wide association study (GWAS) incorporating BOA-specific effects, revealing several genes with BOA-specific effects. Notably, the CGGBP1 gene exhibited a significant effect on TSS only when alleles originated from Brahman. Conversely, the PLK1 gene was significant for TSS when alleles originated from Angus. Both CGGBP1 and PLK1 interact with heat shock proteins during heat stress, these findings reveal different genetic mechanisms for controlling internal body temperature. For HL, a significant Brahman-specific effect was found near the PRLR gene, which is known as the gene controlling the SLICK hair phenotype in Criollo cattle. For SWA, an Angus-specific significant association was found with the PDE4D gene. PDE4D interacts with the cAMP pathway which regulates sweat gland growth and sweat production. These findings underline the genetic complexity of thermotolerance in composite cattle and the crucial role of BOA in identifying key QTL. The study offers novel insights into the genetic mechanisms of thermotolerance, providing a foundation for breeding strategies aimed at improving heat resilience in cattle in subtropical and tropical environments.
PSV-1 Trio-binning Assemblies of the Duroc and Landrace swine breeds
Authors: Ackerson Leland K , Kuhn Kristen , Gondro Cedric , Jiang Jicai , Maltecca Christian , Rohrer Gary A , Rosen Benjamin D , Smith Timothy , Tuggle Christopher K , Huang Wen 
Published: September 2024

Abstract
The current swine reference genome, based on a single Duroc individual, has contributed to many significant advances but also carries limitations in many applications. Reference alleles receive substantial bias from alignment-based approaches. Additionally, structural DNA variants are difficult to identify and represent relative to the linear reference genome. As a result, DNA variants more likely to affect complex quantitative traits are understudied and warrant further investigation. In this study, a trio-binning approach was utilized to produce haplotype-resolved assemblies of a Duroc x Landrace hybrid. The Duroc sire and Landrace dam were sequenced via short-read technology (Illumina), and the hybrid offspring was sequenced via long-read technology (PacBio HiFi). A total of 117 Gb HiFi data was produced, equivalent to approximately 47X coverage of the swine genome. Two highly contiguous and high-quality assemblies were produced using hifiasm. The assembled maternal (Landrace) and paternal (Duroc) genomes had a contig N50 of 76.7 Mb and 55.0 Mb, respectively, both of which surpass that of the current reference genome Sscrofa11.1 (48.2 Mb). Furthermore, the maternal and paternal genomes contained 113.6 Mb and 116.0 Mb of novel sequences relative to the reference, respectively. The Benchmarking Universal Single-Copy Orthologue (BUSCO) scores were approximately 96%, indicating high completeness. The computed assembly QVs were found to be &gt;Q40. Compared with short-read technology, whole genome mapping identified substantially more large SVs (&gt; 50bp). These haplotype-resolved assemblies and additional existing assemblies will serve as the basis for the production of a swine pangenome.
PSV-15 Evaluating the relationship between subcutaneous backfat thickness and sperm morphology in young beef bulls
Authors: Smith Molly , Aguilar Jorge Octavio Solano , Nyhuis Grace , Henry Francine M , Stewart Lawton , Duggin Jason , Fontes Pedro 
Published: September 2024

Abstract
Literature indicates that high-energy diets can lead to reductions in both sperm motility and morphology in bulls. This study aimed to investigate the relationship between individual variation in subcutaneous backfat thickness (SCBF) and sperm morphology in young beef bulls exposed to the same diet. We hypothesized that bulls with excessive subcutaneous fat thickness have increased sperm morphology defects compared with bulls with adequate subcutaneous backfat thickness. Historical data collected from yearling Bos taurus beef bulls (n = 557) enrolled in a bull development program were used in an observational retrospective cohort study to test this hypothesis. Over the course of 5 yr, bulls in two locations were developed according to industry standard practices, and performance was evaluated over 84 d with a 21-d adaptation period. At the end of the performance evaluation period, a carcass ultrasound was performed to evaluate ribeye area, SCBF, and intramuscular fat. Furthermore, breeding soundness examinations (BSE) were performed according to the Society of Theriogenology guidelines within 40 d after carcass ultrasonography. Bulls that failed the BSE for reasons unrelated to semen quality were excluded from this study. Within each year, bulls were ranked based on SCBF and classified as top 10% (TOP; n = 55), middle 80% (MID; n = 446), and bottom 10% (BTM;n = 56) for SCBF. Initial body weight (BW) was greater (P &lt; 0.01) in TOP bulls compared with MID and BTM (Table 1). Off-test BW was also greater in TOP compared with MID and BTM bulls (P &lt; 0.01). In contrast, average daily gain and scrotal circumference did not differ between experimental groups (P = 0.35 and P = 0.65, respectively). TOP bulls had greater (P &lt; 0.01) SCBF compared with MID and BTM, and MID bulls had greater (P &lt; 0.01) SCBF compared with BTM bulls. Similar results were observed for intramuscular fat (P &lt; 0.01) and ribeye area (P &lt; 0.01). Percentage of normal sperm cells was greater in both BTM and MID bulls compared with TOP bulls (P &lt; 0.01). Additionally, percentage of primary abnormalities tended (P = 0.07) to be greater in TOP bulls compared with BTM and MID. There were no differences in the percentage of secondary abnormalities between experimental groups (P = 0.45). There was a tendency (P = 0.07) for a greater percentage of TOP bulls to fail the BSE compared with MID and BTM bulls. Moreover, there was a positive linear relationship (P = 0.01) between SCBF and the probability of failing the BSE. In summary, elevated SCBF in bulls exposed to the same diet was associated with an increase in sperm morphological abnormalities and tended to increase the percentage of bulls failing the BSE.