bluuebunny/crossref_metadata_2025_split huggingface dataset:
231 Anomaly detection for breed purity analysis
Authors: Jiang Xiaohan , Steibel Juan P 
Published: May 2024

Abstract
Recent advancements in genotyping technologies have revolutionized our ability to estimate breed composition in pigs. The classic compositional regression used for this purpose requires a multibreed panel to detect crossbreeding and its application is limited to breed in the panel. In this study, we presented a protocol based on classic anomaly detection algorithms that use single breed panels to detect crossbreeding. By utilizing these methods, we aim to identify and assess breed outliers within large pig genotype panels. The dataset consisted of 44,616 SNP genotypes recorded in purebred Large White, Landrace, Duroc, Pietrain (n = 2,000 from each breed) and 1,010 crossbred pigs (50% Pietrain, 25% Large White, 25% Landrace). Large White pigs (n = 1,500) were randomly selected as reference set. The remaining 500 Large White pigs, other purebred pigs, crossbred pigs, and simulated crossbred animals of known proportion of Large White segments were test sets. We applied two anomaly detection methods: 1) Principal Component Analysis (PCA) and 2) deep learning autoencoders (AE). For PCA the top 600 eigen vectors capturing 85% cumulative proportion of variance in the reference set were selected. Test set genotypes were projected onto the principal components and then they were reconstructed to the full genotype set. For AE, we used a previously published sparse convolutional denoising autoencoder (SCDA) that consisted of two main components: an encoder and a decoder. The encoder compressed the genotypes to 128 components and the decoder reconstructed the set to the original 44,616 SNP. We utilized the model trained in the reference set to reconstruct test set genotypes of the same breed, of alternative breed and of crossbred. Accuracy of reconstruction of genotypes was computed using correlation and mean square error. The proportion of rejected genotypes was used to assess the ability of anomaly detection algorithms to detect crossbreeding. For each criterion, the threshold to reject genotypes was selected as the value at which 5% of Large White animals were rejected (specificity = 0.95). Results are summarized in (Table 1). PCA provided better properties to detect genomic outliers compared with AE. PCA anomaly detection was able to detect purebred individuals with probability 1.0. It also detected over 90% of crossbred individuals that were 75% Large Whites. Crossbred with a lower proportion of Large White genomic segments were detected with P &lt; 0.5. Anomaly detection algorithms can be used to detect genomic outliers but with relatively low sensitivity. More work is needed to optimize these algorithms for breeding applications.
98 Adding parasite resistance to the breeding objective in hair sheep
Authors: Forbes Robert M , Murphy Tom W , Burke Joan M , Lewis Ronald M 
Published: May 2024

Abstract
Economic selection indexes provide the best method to achieve genetic gain for multiple traits simultaneously. Hair sheep enterprises, particularly in environments with substantial gastrointestinal nematode challenge, may benefit from incorporating parasite resistance in a selection index. However, obtaining the relative economic value (REV) for parasite resistance is challenging; information on its impact on productivity is incomplete, as are the costs of treatment given anthelmintic resistance. The National Sheep Improvement Program (NSIP) currently provides producers with an index designed to increase total weight of lamb weaned per ewe lambing (TW). Our objective was to assess the effects of including fecal egg count, an indicator of parasite resistance, as an additional goal trait. Including the benchmark scenario with TW as its sole objective, 10 indexes were constructed using standard index theory. Post-weaning fecal egg count (PFEC) was added to this breeding objective with a REV of -1 and the REV for TW was varied from +1 to +5 at +0.5 increments. Weaning weight, number of lambs born and weaned, and PFEC were the selection criteria, modelled as either phenotypes or estimated breeding values (EBV). Phenotypes and EBV were simulated for 1,000 lambs by Cholesky decomposition and used to generate index scores. Ten replicates were run and the top 3% of males and 26% of females were retained on index scores. Annual responses in the goal traits were estimated. Responses in PFEC were expressed as a percentage, assuming a mean PFEC of 2,089 eggs/g as in NSIP. Concordances with those selected in the benchmark scenario were determined. Using EBV as selection criteria, TW increased by 1.7 kg/yr in the benchmark scenario (Table 1). However, unfavorably, PFEC increased by 2.3%/yr. When phenotypic criteria were used, TW increased by 0.5 kg/yr, and PFEC by 0.3%/yr. Once added to the breeding objective, PFEC decreased regardless of the REV of TW. However, response in TW also reduced, although less so as its REV increased. With EBV as the criteria, the REV of +3 for TW appeared preferable: PFEC reduced by 7.1%/yr with 98% of the response in TW retained. With phenotypic selection criteria, PFEC reduced by 5.2%/yr with 94% of the response in TW retained. With +3 REV for TW and EBV as the selection criteria, on average 65% and 82% of males and females, respectively, were chosen in common with the benchmark. When phenotypic criteria were used, those percentages were 60% and 80%, respectively. Implementing a more holistic index with REV of +3 for TW and -1 for PFEC would result in reasonable responses in both traits. However, producers will need to decide if reduced gains in TW is acceptable to improve parasite resistance in a hair sheep breeding program.
70 Determination of phosphorus release of Microtech phytase in nursery pig diets
Authors: Navales Ron Aldwin S , Gaffield Katelyn , Kim Ty , DeRouchey Joel M , Martin Paul , Javierre Juan , Gebhardt Jordan T , Goodband Robert D , Tokach Mike D , Woodworth Jason C 
Published: May 2024

Abstract
A total of 320 barrows (DNA 241 × 600; initially 10.7 ± 0.21 kg) were used in a 21-d growth trial to determine the available P (aP) release curve for Microtech phytase (Guangdong VTR Bio-Tech Co, Ltd. Zhuhai, Guangdong, China). At approximately 21 d of age, pigs were weaned and randomly allocated to pens and fed a common diet for 18 d and then fed a P depletion diet (0.11% aP) for 3 d. On d 21 post-weaning, considered d 0 of the study, pigs were blocked by average pen body weight (BW) and randomly allotted to 1 of 8 dietary treatments with 5 pigs per pen and 8 pens per treatment. Dietary treatments were derived from a single basal diet and ingredients including phytase, monocalcium P, limestone, and sand were added to create the treatment diets. Treatments include 3 diets with increasing aP (0.11, 0.19 and 0.27%) using monocalcium phosphate that were used to develop the standard curve and 5 diets with 0.11% aP and increasing phytase (250, 500, 1,000, 1,500 and 2,000 FTU/kg) that were used to develop the aP release curve. Pigs were weighed weekly and feed disappearance was recorded per pen for the calculation of average daily gain (ADG), average daily feed intake (ADFI) and gain to feed ratio (G:F). At the conclusion of the experiment, 1 pig, closest to the mean weight of each pen, was euthanized for bone analysis. The right fibula, rib, and metacarpal were collected for the determination of bone density, bone ash weight, and bone ash percentage. Pigs fed diets with increasing aP from inorganic P had improved (quadratic, P ≤ 0.05) final BW, ADG, and G:F (Table). Pigs fed diets with increasing phytase had linearly increased (P &lt; 0.01) final BW and ADFI and quadratically increased (P ≤ 0.04) ADG and G:F. Bone density, bone ash weight, and bone ash percentage increased linearly (P &lt; 0.01) with increasing aP from inorganic P and increasing phytase. Results were used to determine release values for Microtech phytase for each response criteria as shown in the table. The aP release quadratically increased (P ≤ 0.02) with increasing phytase when growth performance was used as response criteria and linearly increased (P &lt; 0.01) when bone characteristics were used as response criteria. The available P release curve developed for Microtech phytase for percentage bone ash using combined data generated from all three bones is: aP = (0.868 × FTU/kg) ÷ (9,599.511 + FTU/kg).
68 Serological comparisons of IBR-BVD-PI3-BRSV- Mannheimia haemolytica toxoid vaccines
Authors: Midkiff Kirsten A , Kegley Beth B , Gadberry Shane , Cheek Robin A , Reynold Jana L , Hess Tom , Sarchet Jeff , Blanding Mitch , Short Tom , Powell Jeremy G 
Published: May 2024

Abstract
The objective of this study was to compare serological responses in low-risk calves vaccinated with various IBR-BVD-PI3-BRSV-Mannheimia haemolytica toxoid vaccines. Bovine herpes virus-1 (BHV-1) and M. haemolytica (MH) leukotoxin titers were analyzed to investigate any potential BHV-1 antigen interference to MH leukotoxin levels when administering multi-valent vaccines. Serology responses of BVD, BRSV, and PI3 were not within the scope of this study. Before enrolling in the study, weaned calves born to dams at two University of Arkansas beef cattle research stations that were not previously vaccinated with MH toxoid or BHV-1 were bled and sera harvested. Crossbred steer and heifer calves [n = 364; steers = 168, heifers = 196; body weight (BW) = 187.9 ± 2.8 kg] were used for this study at the two locations. Calves were stratified by MH titers, BHV-1 titers, and sex, and allotted to 1 of 5 treatments: 1) “BS GOLD” = IBR-BVD-PI3-BRSV-MH (Bovi-Shield GOLD One Shot, 2 mL/SQ; Zoetis); 2) “P5 + PRE” = IBR-BVD-PI3-BRSV-MH (Pyramid 5 + Presponse SQ, 2 mL/SQ; Boehringer Ingelheim Animal Health); 3) “BV Once” = IBR-BVD-PI3-BRSV-MH-PM (Bovilis Vista Once SQ, 2 mL/SQ; Merck Animal Health); 4) “IF3 + One Shot” = IBR-BVD-PI3-BRSV (Inforce 3, 2 mL/intranasal; Zoetis) and BVD-MH (One Shot BVD, 2 mL/SQ; Zoetis); and 5) “BN + BV” = IBR-BVD-PI3-BRSV (Bovilis Nasalgen 3-PMH, 2 mL/intranasal; Merck Animal Health) and BVD (Bovilis Vista BVD CFP, 2 mL/SQ; Merck Animal Health). Cattle were weighed on d 0, 7, 14, and 28 and blood samples were taken for MH leukotoxin titers. Serum samples were collected on d 0 and 28 for BHV-1 titers. For statistical analyses, data were analyzed using the PROC MIXED procedure of SAS. Statistical significance was determined at P ≤ 0.05, with tendencies at 0.05 &lt; P ≤ 0.1. There was an overall treatment effect for MH serum antibody titers with BV Once and BN + BV vaccinated calves exhibiting decreased MH serum titers compared with calves vaccinated with BS GOLD, P5 + PRE, and IF3 + One Shot (P = 0.0457). There was a treatment by day interaction for BHV-1 titers (P = 0.0336). On d 28, BHV-1 serum titers were greatest in BS GOLD and BN + BV vaccinated calves, least in calves that received IF3 + One Shot vaccines, and intermediate for BV Once vaccinated calves. Morbidity and average daily gain did not differ between treatments (P &gt; 0.27) throughout the 28-d study period.
65 Effect of two different implant programs on growth performance and carcass characteristics in beef steers fed to three differing harvest endpoints
Authors: Francis Becca Grimes , Hutcheson John P , Walter Lee-Anne J , Nichols Wade T , Smith Zachary K 
Published: May 2024

Abstract
Two implant programs (Merck Animal Health, DeSoto, KS and Zoetis, Parsippany, NJ) and 3 d on feed (DOF) endpoints were used to evaluate growth performance and carcass characteristics of finishing beef steers. Beef steers [n = 480; initial body weight (BW) = 402; SEM = 2.4 kg] were assigned to treatment pens (10 steers/pen) with pen (n = 48 pens total) as the experimental unit. Treatments were arranged as a 2 x 3 factorial including implant program: 1) a single Revalor-XS (200 mg trenbolone acetate and 40 mg estradiol-17β total) on d 0 (XS) compared with 2) Synovex-Choice (100 mg trenbolone acetate and 14 mg estradiol benzoate) on d 0 and re-implanted with a Synovex-ONE Feedlot (200 mg trenbolone acetate and 28 mg estradiol benzoate) 70 d later (CHSOF) and harvest endpoint: 1) 162 DOF, 2) 183 DOF, or 3) 204 DOF. Both implant groups were removed from their pens on the day of reimplantation. Data were analyzed as a RCBD. Final BW was calculated as HCW/0.625. An implant × DOF (P ≤ 0.04) interaction was noted for gain to feed ratio (G:F), REA, final BW adjusted to 28% estimated empty body fatness (AFBW), and USDA quality grade distribution, a tendency for an interaction was observed for final BW, average daily gain (ADG), HCW, and dressing percentage (P ≤ 0.09), no other interactions were noted for any traits evaluated (P ≥ 0.17). Steers from CHSOF/162 had increased G:F by 4.1 to 6.5% compared with others (P ≤ 0.05). Steers from XS/204 had greater REA by 3% to 10% (P ≤ 0.05) compared with all other treatments and greater AFBW by 3% to 7% (P ≤ 0.05), compared with all other treatments except CHSOF/204. Steers from XS had a greater proportion of carcasses grading USDA Prime at 162 and 183 DOF compared with CHSOF. As a result of increased DOF, the XS/204 and CHSOF/204 steers had greater final BW and HCW compared with all other treatments (P ≤ 0.05), steers from XS/183 had greater HCW than XS/162 and CHSOF/162; however, CHSOF/183 did not differ from CHSOF/162 (P ≤ 0.05). Steers from CHSOF/162 had greater ADG by 5.8% compared with CHSOF/183 (P = 0.05), while all others were intermediate. Dressing percentage was the greatest for XS/204 and least for CHSOF/183 (P ≤ 0.05). Cattle from XS had increased (P &lt; 0.01) DMI by 2.6%. As DOF increased, carcass-adjusted final BW increased while ADG decreased (linear; P = 0.05). As DOF increased, REA and AFBW increased (P &lt; 0.01). Increasing DOF, increased (P &lt; 0.01) USDA yield grade 4 and 5 carcasses and decreased yield grade 2 and 3 carcasses. Implant strategy had a marginal influence on growth performance and carcass characteristics; however, as DOF increased carcass weights, rib fat, and ribeye area increased.
11 The effect of increased standardized ileal digestible lysine through increased soybean meal during late gestation on lactating sow and litter performance
Authors: Jenkins Abigail K , Woodworth Jason C , Gebhardt Jordan T , DeRouchey Joel M , Tokach Mike D , Goodband Robert D 
Published: May 2024

Abstract
A total of 87 sows (Line 241, DNA) and their offspring were used to evaluate the effect of increasing standardized ileal digestible (SID) lysine through increasing soybean meal (SBM) concentration in late gestation diets on lactating sow and litter performance. Sows were blocked by parity and body weight (BW) on approximately d 90 of gestation and allotted to 1 of 3 treatments with 29 replications per treatment. Diets included increasing SID lysine (0.60, 0.80, or 1.00%) through increased SBM (14, 21, or 29% of the diet). Sows received approximately 2.04 kg/d of their treatment diet for an average SID Lys intake of 11.9, 15.8, or 19.9 g/d, respectively. Diets were fed from d 90 of gestation until farrowing. After farrowing, all females were fed a common lactation diet containing 1.10% SID Lys until weaning (19 d post-farrow). Sow BW, caliper score, and backfat and loin depth were collected on d 90, upon entry into the farrowing house (d 110), and at weaning. Urine samples were collected on d 90 and 110 of gestation to ascertain urinary creatinine concentrations. Litters were cross-fostered within sow treatment by 48 h after farrowing to equalize litter size. Parity was included in the statistical model as a fixed effect with females being classified as either a primiparous (n = 35) or multiparous (n = 52) sow. Body weight gain from d 90 to 110 of gestation increased as SID Lys increased (linear, P &lt; 0.001; Table). There were no differences in starting litter size or piglet birth weight with increasing SID Lys in late gestation (linear, P &gt; 0.10). Change in urinary creatinine level from d 90 to 110 of gestation tended to decrease as SID Lys increased in the diet (linear, P = 0.063) suggesting that less muscle catabolism occurred with increasing SID Lys. Piglet average daily gain (ADG) from d 2 to 10 of lactation linearly increased as SID Lys increased (P = 0.017), but not from d 2 to weaning. From d 2 until weaning, litters from sows fed the 0.80% SID Lys gestation diet had the greatest litter gain (quadratic, P = 0.044). Pre-weaning mortality from birth until d 2 of lactation was greatest for sows fed 0.80% SID Lys (quadratic, P = 0.025). There was a parity × gestation diet interaction for pre-weaning mortality from d 2 to weaning (P = 0.049) where mortality increased as SID Lys increased in primiparous sows but decreased in multiparous sows. In conclusion, increased SID Lys through increased SBM linearly increased late gestation sow BW gain and piglet ADG during the first portion of lactation. However, litters from sows on the 0.80% SID Lys treatment exhibited the highest litter ADG during late lactation and overall.
18 Effect of precision feeding standardized ileal digestible lysine to lactating sows compared with conventional feeding strategies in a commercial farm
Authors: Spinler Mikayla , Gebhardt Jordan T , DeRouchey Joel M , Tokach Mike D , Goodband Robert D , Frobose Hyatt , Uitermarkt Amanda , Moita Vitor , Woodworth Jason C 
Published: May 2024

Abstract
A total of 728 sows and litters were used in a 19-d lactation study to evaluate effects of precision feeding SID Lys and other amino acids on sow and litter performance and feed cost in a commercial farm. Sows were blocked by parity and allotted to 1 of 2 treatments at entry into farrowing. Treatments consisted of a control diet or a feed blending curve. Two diets were used to create treatment curves, a low Lys diet (0.60% SID Lys) or a high Lys diet (1.07% SID Lys). Sows on the control treatment were fed only the high Lys diet and sows on the blend curve were fed a blend of the low and high Lys diets using the Gestal Quattro Opti Feeder (Jyga Technologies, St-Lambert-de-Lauzon, Quebec, Canada) to target a specific Lys intake/d. Lysine intake targets were based on the NRC (2012) model requirements, except targets were increased by 20% to reach average Lys intake of approximately 63 g/d. The blend of the low and high Lys diet was adjusted on d 7 and 14 for sows fed the blend curve in an attempt to reach target Lys intake. Average Lys intake was 87% of target Lys intake because feed intake was lower than predicted. Sows fed the control diet had greater (P &lt; 0.001; 72.0 vs 54.8 g/d) Lys intake compared with sows on blend curves because they were fed only the high Lys diet (Table). No differences (P &gt; 0.05) in body weight (BW), backfat, loin depth, caliper score, or average daily feed intake (ADFI) were observed. There were no differences (P &gt; 0.05) in litter size at d 2 after equalization or weaning; however, piglets and litters from sows fed the control treatment tended to have greater weaning weights (P = 0.090) and average daily gain (ADG; P = 0.071) compared with piglets and litters from sows fed the blend curve, likely due to insufficient Lys intake for sows on the blend curve to maximize litter growth performance. Feed cost per sow was less (P &lt; 0.05) for sows fed the blend curve in both a low and high ingredient price scenario. No differences (P &gt; 0.05) in feed cost per kg of litter weight gain were observed; however, feed cost per weaned pig was less (P &lt; 0.05) for sows on the blend treatment. Serum urea nitrogen was greater (P &lt; 0.05) at weaning compared with d 10 for control fed sows and was greater (P &lt; 0.05) than blend-fed sows at both time points. Sows fed the control diet had greater milk crude protein (P = 0.05) compared with sows fed the blend curve. While precision feeding sows using diet blending during lactation can be used to reduce feed cost, future research should focus on using technology to automatically adjust diet blend for low or high-feed intake sows to avoid the over or under-feeding of nutrients.
28 Investigation of protein deposition pattern of PIC337×Camborough commercial pigs
Authors: Lu Ning , Zeng Nanfang , Su Ning , Chen Ling , Chen Jie , Vier Carine M , Cast Wayne R , Dritz Steve , Wilson-Wells Danielle , Zaragoza Luis E , Camp Jordi , Orlando Weasley A 
Published: May 2024

Abstract
The objective of the trial was to investigate the protein deposition pattern of PIC337×Camborough commercial pigs. A total of 1,064 barrows and gilts [PIC337×Camborough, initial body weight (BW) = 6.0 ± 0.1 kg] were used in the trial with 38 mixed sex pens, 28 pigs per pen. At the beginning of the trial, the lightest 10% of the barrows and gilts were selected and placed in four pens (equal numbers of barrows and gilts within a pen), and the remaining pigs were randomly placed into the other pens (equal numbers of barrows and gilts within a pen). A common 6-phase corn-soybean based wean-to-finish diets were fed throughout the trial. Dietary net energy and standardized ileal digestible lysine levels were (6-10 kg BW: 2,600 Kcal/kg and 1.35%; 10-20 kg BW: 2,520 Kcal/kg and 1.30%; 20-38 kg BW: 2,470 Kcal/kg and 1.20%; 38-72 kg BW: 2,450 Kcal/kg and 0.98%; 72-127 kg BW: 2,450 Kcal/kg and 0.87%; and 127-149 kg BW: 2,450 Kcal/kg and 0.77%). On d 97 after placement, 5 barrows and 5 gilts with BW close to pen average were selected for individual BW by a portable scale and 10th rib backfat and loin depth measurements (ExaGo portable ultrasound scanner, Imv imaging, UK). Then on d 111, 117, 136, 142, and 167 after placement, the same 5 barrows and 5 gilts were measured for individual BW, 10th rib backfat and loin depth. The fat-free lean mass is estimated by the equation 6.783-0.6198×(10th rib backfat depth, mm)+0.1578×(10th rib loin depth, mm)+1.0362×(warm carcass weight, kg). A constant carcass yield of 75% was used to estimate warm carcass weight. Data were analyzed using a linear mixed model in R Studio (Version 3.5.2, R Core Team; Vienna, Austria). The average BW of pigs at the 6 measurements were: 77.2, 92.4, 99.2, 122.5, 128.0, and 153.6 kg, respectively. The average daily gain (ADG) was 1,139, 1,155, 1,145, 1,126, and 977 g/d for 77.2 to 92.4 kg BW, 92.4 to 99.2 kg BW, 99.2 to 122.5 kg BW, 122.5 to 128.0 kg BW, and 128.0 to 153.6 kg BW, respectively. The average daily 10th rib backfat depth gain was 0.05, 0.08, 0.15, 0.17, and 0.20 mm/d. The average daily 10th rib loin depth gain was 0.42, 0.43, 0.41, 0.39, and 0.23 mm/d. The average daily fat-free lean mass gain (ADFFLG) was 547, 551, 528, 515, and 422 g/d. The fitted quadratic model for ADG is 83.57782 + 19.90632 × (BW, kg)-0.09176×(BW, kg)2, and the calculated maximum ADG was 1,163 g/d when BW was 108.5 kg. The fitted quadratic model for ADFFLG is 85.90926 + 9.23773 × (BW, kg) - 0.04591 × (BW, kg)2, and the calculated maximum ADFFLG is 550.6 g/d when BW was 100.6 kg. Under the conditions of the current trial, PIC337×Camborough pigs reaches the maximum rate of protein deposition at BW between 100.6 and 108.5 kg.