bluuebunny/crossref_metadata_2025_split huggingface dataset:
31 Building a functional annotation of the equine genome
Authors: Petersen Jessica L , Finno Carrie J , Bellone Rebecca R , Burns Erin N , Kingsley Nicole B , Kalbfleisch Ted , MacLeod James N , Creppe Catherine , Miller Donald C , Antczak Douglas F 
Published: July 2019

Abstract
The molecular determination of complex traits related to animal production, health, and performance remains elusive. In response, an international effort (Functional Annotation of ANimal Genomes, or FAANG) was initiated with the goal of identifying functional elements of the genome across domestic animal species. Toward this goal, the equine FAANG community has developed a biobank of over 80 tissues, four fluid types, and nine microbiome samples collected from two adult Thoroughbred mares as a resource for functional annotation of the horse genome. Full clinical phenotyping and careful histologic evaluation was performed on each tissue to allow for correlation of any observed pathologies and cell composition with sequencing results. Whole-genome sequencing (WGS) of each horse is complete as is RNA-sequencing (mRNA and smRNA) and analysis from eight prioritized tissues (liver, lung, hoof lamina, heart, longissimus dorsi muscle, ovary, parietal cortex, and adipose) as well as from 30 additional tissues sequenced with support from members of the community (known as the “Adopt-a-tissue” initiative). All sequencing data are now publicly available. Chromatin shearing and antibody concentrations have been optimized for ChIP-seq to characterize the major histone modification marks (H3K4me1, H3K4me3, H3K27me3, H3K27ac) in the eight prioritized tissues and spleen. Data collection and analyses are nearly complete. Assays to identify genomic insulators denoted by CCCTC-binding sites are also underway as is optimization of ATAC-seq, to characterize open chromatin in select tissues. The biobank’s use has extended to include chromatin run-on and sequencing (ChRO-seq) assays allowing for a novel comparison with ChIP-seq peaks. Further extensions of the biobank include keratinocyte cell culture, centromere mapping, karyotype analyses, methylation profiles, and microbiome characterization. These data provide a valuable baseline of genome function in the healthy, adult Thoroughbred mare and will allow for an improved understanding of and continuing research on tissue-, developmental-, and disease-associated genome regulation.
47 Young Scholar Presentation: Meta-regression analysis to predict the influence of branched-chain and large neutral amino acids on growth performance of pigs
Authors: Cemin Henrique S , Tokach Mike D , Dritz Steve S , Woodworth Jason C , DeRouchey Joel M , Goodband Robert D 
Published: July 2019

Abstract
Excess of a branched-chain amino acid (BCAA), particularly Leu, may result in increased degradation of the others due to common catabolic steps. Moreover, large neutral amino acids (LNAA) and BCAA have common brain transporters. Therefore, excessive BCAA may decrease the absorption of AA that serve as precursors of neurotransmitters. We hypothesize that practical diets with high levels of feed-grade AA can potentially create BCAA imbalances and impact performance. A meta-regression was conducted to evaluate the effects of BCAA and their interactions with LNAA to develop prediction equations for ADG, ADFI, and G:F. Data from 25 papers for a total of 44 trials were recorded in a database. Diets were reformulated using NRC (2012) nutrient values. Amino acids were expressed on standardized ileal digestible basis. A step-wise manual forward selection was used to evaluate predictor variables. Predictors had to be significant (P < 0.05) as a single variable predictor and provide a BIC improvement of at least 2 points to be included in the model. Observations were weighted using the inverse of the squared SEM. The resulting predictor equations were: ADG, g = – 985.94 + (15.2499 × average BW (kg)) – (0.08885 × average BW × average BW) + (1.063 × Leu:Lys) + (20.2659 × Ile:Lys) – (0.1479 × Ile:Lys × Ile:Lys) + (9.2243 × (Ile+Val):Leu) – (0.03321 × (Ile+Val):Leu × (Ile+Val):Leu) – (0.4413 × Ile:Trp); G:F = 648.3 – (6.2974 × average BW (kg)) + (0.02051 × average BW × average BW) + (0.5396 × Ile:Lys) + (1.7284 × Val:Lys) – (0.00795 × Val:Lys × Val:Lys) – (1.7594 × Met:Lys); and ADFI, kg = predicted ADG/predicted G:F. The equations suggest that increasing Leu:Lys negatively affects ADG due to a reduction in ADFI and G:F. The addition of Val, Ile, and Trp, alone or in combination, has the potential to counteract the negative effects of high Leu on growth performance.
52 Young Scholar Presentation: Maternal supply of methionine during late-pregnancy alters in utero and neonatal development, hepatic one-carbon metabolism,and innate immune response in Holstein calves
Authors: Alharti A S , Loor Juan , Batistel Fernanda , Ballou Michael A , Parys Claudia , Pan X Y , Trevisi Erminio 
Published: July 2019

Abstract
Pregnancy and early life are critical periods of plasticity during which the fetus and neonate may be influenced by environmental factors such as nutrition. Objectives were to investigate if increasing methionine (Met) supply during late-pregnancy affects developmental, metabolic, and immune parameters of the calf at birth and during the neonatal period. Calves born to Holstein cows individually-fed a basal control (CON; 1.47 Mcal/kg dry matter [DM] and 15.3% crude protein) diet with no added Met or CON plus rumen-protected Met (MET; Mepron® at 0.09% of diet DM) during the last 28±2 d of pregnancy were used. Liver biopsies were harvested at 4, 14, 28, and 50 d of age and used for metabolomics via GS-MS and activity of hepatic 1-carbon metabolism enzymes. Blood for biomarker analyses and innate immune function assays was harvested at birth (before colostrum feeding), 7, 21, 42 and 50 d of age. Whole blood was challenged with enteropathogenic bacteria (E. coli 0118:H8), and phagocytosis and oxidative burst of neutrophils and monocytes quantified by flow cytometry. At birth, MET calves had greater (P≤0.05) body weight (BW, 44.1 vs. 42.1±0.70 kg), hip height (HH, 81.3 vs. 79.6±0.53 cm), and wither height (WH, 77.8 vs. 75.9±0.47 cm). Differences persisted through 9 wk of age, resulting in average responses of +3.1 kg BW, +1.9 cm HH, and+1.8 cm WH in MET compared with CON. Average daily gain during the 9 wk was (P<0.05) 0.72±0.02 kg/d in MET and 0.67±0.02 kg/d in CON calves. Despite similar rates of daily DMI, maternal supplementation with Met led to greater (P ≤ 0.05) overall hepatic concentrations of the 1-carbon metabolism intermediates adenosine, betaine, choline, glycine, and N,N-dimethylglycine in liver tissue. Among transsulfuration pathway metabolites, concentrations of cystathionine, cysteinesulfinic acid, hypotaurine, serine, and taurine were greater (P ≤ 0.05) in MET calves. There was a treatment × day effect for activity of betaine-homocysteine S-methyltransferase (BHMT), methionine synthase (MTR) and cystathionine-beta-synthase (CBS) in liver tissue. Activity of BHMT and CBS increased in MET calves between d 4 and 14, with a peak at 28 d. Despite a linear increase from d 4 to 28, activity of MTR in MET calves was lower on d 4 and 50. Plasma concentrations of haptoglobin and activity of myeloperoxidase in both maternal groups increased (P ≤ 0.05) markedly between 0 and 7 d of age followed by a decrease to baseline at d 21 with responses being lower in MET compared with CON calves. In vitro phagocytosis in stimulated neutrophils was greater overall (P ≤ 0.05) in MET calves. Overall, data indicate that increasing the maternal supply of Met during late-pregnancy benefits calf growth in part through alterations in hepatic metabolism and innate immune response.
Effect of different fat sources and vitamin E status/levels on growth performance, antioxidant status, carcass characteristics, fatty acid profile, and meat quality of pigs grown to heavy slaughter weight at 150 kg
Authors: Wang Ding , Jang Young Dal , Rentfrow Gregg K , Monegue Harold J , Azain Michael , Lindemann Merlin 
Published: July 2019

Abstract
Two experiments were used to evaluate the potential interaction of fat source and vitamin E (VE) in heavy slaughter weight pigs. In Experiment 1, a total of 64 individually-fed pigs (28.41 ± 0.83 kg) were randomly assigned to 8 dietary treatments in a 4×2 factorial arrangement. Fat treatments included cornstarch (CS), tallow (TW), corn-oil (CO), and coconut-oil (CN). VE treatments were dietary α-tocopheryl-acetate (ATA) at 11 and 200 ppm. In Experiment 2, a total of 72 individually fed pigs (28.55 ± 1.16 kg) were randomly assigned to 12 dietary treatments in a 2×6 factorial arrangement. Fat treatments were TW and CO. VE treatments included four levels of ATA (11, 40, 100, and 200 ppm) and two levels of mixed tocopherols (primarily γ-tocopherol; 40 and 100 ppm). VE deposition, growth performance, and meat quality were measured in both experiments. In both experiments, interaction between fat sources and VE were detected (P < 0.01) on plasma VE concentration, which increased (P < 0.01) with time and with increasing dietary VE, but increased faster (P < 0.05) in pigs fed with CN and TW compared to pigs fed CS and CO. Compared to CO, more saturated dietary fat sources (CN and TW) led to firmer belly (P < 0.01), which had more (P < 0.01) SFA and MUFA while less (P < 0.01) PUFA. In Experiment 1, increasing dietary ATA decreased (P < 0.05) FCR in Phase 4 and Phase 5. In Experiment 2, increasing dietary ATA increased overall ADG (linear, P = 0.02), with an interaction (P < 0.05) with fat sources on cumulative ADG during Phase1-4, wherein pigs fed CO, but not TW, had increased ADG with increasing dietary ATA. Increasing dietary ATA increased (quadratic, P < 0.05) liver SOD activity, and decreased (quadratic, P < 0.05) liver MDA content. The oxidative stability of loin was improved (P < 0.01) when dietary ATA increased over 40 ppm. In summary, both dietary fat source and VE supplementation affected the response measures.
Nutritional intervention for the intestinal development and health of weaned pigs
Authors: Liu Yanhong 
Published: July 2019

Abstract
Weaning imposes simultaneous stress, resulting in reduced feed intake and growth rate and increased morbidity and mortality of weaned pigs. Weaning impairs the intestinal integrity, disturbs digestive and absorptive capacity, and increases the intestinal oxidative stress and susceptibility of diseases in piglets. The improvement of intestinal development and health is critically important for enhancing nutrient digestibility capacity and disease resistance of weaned pigs, therefore, increasing their survival rate at this most vulnerable stage and overall productive performance during later stages. A healthy gut may include but not limited several important features: a healthy proliferation of intestinal epithelial cells, an integrated gut barrier function, a preferable or balanced gut microbiota, and a well-developed intestinal mucosa immunity. Burgeoning evidence suggested nutritional intervention are one of promising measures to enhance intestinal health of weaned pigs, although the exact protective mechanisms may vary and are still not completely understood. Previous research indicated that functional amino acids, such as arginine, cysteine, glutamine, or glutamate, may enhance intestinal mucosa immunity (i.e. increased sIgA secretion), reduce oxidative damage, stimulate proliferation of enterocytes, and enhance gut barrier function (i.e. enhanced expression of tight junction protein) of weaned pigs. A number of feed additives are marketed to assist in boosting intestinal immunity and regulating gut microbiota, therefore, reducing the negative impacts of weaning and other environmental challenges on piglets. The promising results have been demonstrated in antimicrobial peptides, clays, direct-fed microbials, micro-minerals, milk components, oligosaccharides, organic acids, phytochemicals, and many other feed additives. This review summarizes our current understanding of nutritional intervention on intestinal health and development of weaned pigs and the importance of mechanistic studies focusing on this research area.
58 Feed, feeding levels, and tissue analytics of vitamins: Observations from the field
Authors: Hinson Buddy , Moser Ronny , Ackerman Matthew , Main Rodger 
Published: July 2019

Abstract
Targeted vitamin inclusion rates within swine diets are typically at levels 2–7 times that of the known published requirements. These increased rates are mainly looked at as an “insurance policy” since very little vitamin research has been conducted in the last two decades and swine growth rates and reproductive traits have increased substantially during this same time. When production issues such as broken bones, downer animals, or sudden deaths occur, vitamin analysis is commonly done on feed, serum, or tissue samples. This discussion will shed light on observations around vitamin analytics that include variation due concentration within product, lab-to-lab variation, and within lab variation. In addition to discrepancies found in feed, serum and liver sample vitamin analytics do not seem to present a clear picture. Across multiple phases of production, these analysis consistently fall well below what would be considered to be reference values that are reported by diagnostic labs. This occurs not only in sick animals but also in animals that appear to be in perfect health and are consuming adequate levels of feed. In order to determine the impact of vitamin supplementation on performance and serum/tissue vitamin status, five trials across sows, nursery, and grow-finish swine were conducted. The goal of these trials is not to determine the various vitamin requirements, but to begin the conversation in order to help establish new reference values that are applicable to today’s genetics, vitamin supplementation levels, and rearing environments. Hopefully this presentation will lead to further questions and discussions within the industry regarding level of vitamin supplementation and the subsequent impacts on performance and serum/tissue vitamin status.
68 Genomic prediction accuracies of vulva size traits in Landrace and Yorkshire gilts
Authors: Corredor Flor Anita , Leach Richard J , Ross Jason W , Keating Aileen F , Serão Nick V L 
Published: July 2019

Abstract
Recent results indicated that vulva size measured prior to puberty may be predictive of reproductive performance in sows. Therefore, the objective of this study was to estimate genomic prediction accuracies for vulva size traits in purebred gilts. A total of 1,185 Landrace (n = 477) and Yorkshire (n = 708) gilts originated from two different lines were used in this study. All animals had vulva size measurements taken at an average 21.5 weeks of age (SD = 5.8). Measurements included vulva width (VW), vulva height (VH), and vulva area (VA). Genotype data (Geneseek GGP-HD) was available for all animals, for ~40K SNPs. Marker allele substitution effects were estimated using Bayes-B (pi = 0.99) in a model including the fixed effects of contemporary group, line, breed (for multi-breed analysis only) and body weight (covariate), and the random effect of SNPs. Genomic prediction accuracies were estimated using three training and validation strategies: between-breed, within-breed (4 and 6 cross-validation folds for Landrace and Yorkshire, respectively), and multi-breed (10-fold cross-validation, using one-fold per breed for validation at a time). Between-breed accuracies were low and consistently negative, with -0.02, -0.10, and -0.05 in Landrace and -0.05, -0.04 and -0.03 in Yorkshire, for VW, VH, and VA, respectively. Within Landrace, these were moderate, with 0.35 (VW), 0.42 (VH), and 0.56 (VA), whereas lower accuracies were obtained for Yorkshire, with 0.07 (VW), 0.20 (VH), and 0.14 (VA). Multi-breed accuracies were low with 0.14 (VW), 0.14 (VH), and 0.24 (VA) for Landrace, and 0.03 (VW), 0.16 (VH), and 0.09 (VA) for Yorkshire. These results indicate that genomic selection for vulva size traits is possible in Landrace, but limited in Yorkshire gilts. The low between- and multi-breed results suggest that QTL for these traits are in opposite phases between breeds and/or do not segregate in both breeds. Financial support from the Iowa Pork Industry Center is appreciated.
76 Effects of replacing monensin and tylosin in finishing cattle diets with essential oils and/or benzoic acid on growth performance and carcass characteristics
Authors: Wang Lydia M , Mandell Ira B , Bohrer Benjamin M 
Published: July 2019

Abstract
This study examined the effects of replacing monensin and tylosin with essential oils and/or benzoic acid in finishing cattle diets on growth performance, feed efficiency, and carcass characteristics. Crossbred steers (n = 68; BW = 539 ± 4 kg) were blocked by starting weight into three blocks and were assigned to 1 of 5 finishing diets: no additional supplement (CON), monensin/tylosin (M/T), essential oils (EO), benzoic acid (BA), or a combination of essential oils and benzoic acid (COMBO). Steers were housed with two dietary treatments represented in seven pens, while an eighth pen only housed steers fed the CON diet. Individual animal feed intake was collected using an Insentec feeding system, so steer was the experimental unit for all analyses. Data were analyzed using a randomized complete block design with fixed effect of treatment and random effect of block. Final weight, average daily gain, and dry matter intake were similar (P > 0.12) among treatments. Gain to feed ratio differed (P = 0.05) among treatments, specifically steers fed the M/T diet had greater G:F compared with steers fed CON, EO, and COMBO diets. For carcass characteristics, there were no significant treatment differences in hot carcass weight (P = 0.19), dressing percentage (P = 0.62), ribeye area (P = 0.49), fat thickness (P = 0.84), calculated yield grade (P = 0.91), marbling score (P = 0.07), and yield grade (P = 0.43). Quality grade differed (P = 0.05) among treatments, with steers fed the EO diet having a lower quality grade than all other dietary treatments. Overall, steers supplemented with essential oils and(or) benzoic acid had similar gain, feed intake, and carcass parameters as steers fed CON, while steers fed M/T had slightly improved feed efficiency compared to all other treatments.
70 Effects of copper, zinc, and manganese intake in late gestation on milk, cow plasma, and calf plasma trace mineral concentrations post-calving in beef cattle
Authors: Stephenson Emma L , Rathert Abigail R , Tucker Heather , Meyer Allison M 
Published: July 2019

Abstract
Multiparous, fall-calving beef cows [n = 48; 649 ± 80 (SD) kg BW; 5.3 ± 0.5 BCS] were individually-fed tall fescue-based hay (12.2% CP, 61.5% NDF) and supplemented to meet/exceed nutrient recommendations except Cu, Zn, and Mn. From approximately 90 d pre-calving to 11 d post-calving, cows received: no additional Cu, Zn, or Mn (CON); Cu, Zn, and Mn sulfates (ITM) or metal methionine hydroxy analogue chelates (CTM, MINTREX®, Novus International) supplying 133% NASEM recommendations; or Cu, Zn, and Mn sulfates and chelates supplying 100% recommendations (reduce and replace, RR). Treatment, sampling day, their interaction, and breeding group were fixed effects with cow as the experimental unit. Colostrum and milk Cu and Mn and plasma Mn were generally not detectable. Colostrum Zn was greater (P ≤ 0.03) in CTM and ITM than CON and RR. All treatments had greater (P < 0.001) colostrum Zn than d 35 milk, which was greater (P ≤ 0.03) than d 60. Treatment did not affect (P ≥ 0.19) cow or calf plasma Cu or Zn post-calving. Calf plasma Zn decreased (P ≤ 0.02) from 0 to 35 d of age. Calf plasma Cu increased (P < 0.01) from 0 to 35 d, then decreased (P = 0.01) from 35 to 60 d. Cow plasma Zn and Cu were greater (P ≤ 0.02) at lactation d 35 and 60 than 1 h post-calving. Pearson correlation coefficients were used to determine relationships among cow and calf mineral status. There were weak positive correlations (P ≤ 0.06) between calf plasma and milk Zn at d 35 and 60. Cow and calf plasma Zn immediately post-calving had a weak negative correlation (P = 0.04). These results indicate greater Zn concentration in beef cow colostrum than milk, and suggest calf circulating Zn is partially dependent on milk Zn concentration.
83 Lifelong dynamics of the swine gut microbiome: from birth to market
Authors: Wang Xiaofan , Tsai Tsung Cheng , Maxwell Charles V , Zhao Jiangchao 
Published: July 2019

Abstract
Despite the recent advances in the swine gut microbiomes during different growth stages, a comprehensive longitudinal study of the lifelong dynamics of the swine gut microbiome is lacking. To fill this gap of knowledge, we selected seventeen piglets (PIC29*380) that were born on the same date from three sows. We collected a total of 274 rectal swabs during lactation (d 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, and 174) stages. Samples were extracted using the Powersoil DNA isolation kit (Qiagen, Hilden, Germany) and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16 S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. In general, alpha diversity including community richness (e.g., number of observed features, Chao1) and diversity (e.g., Shannon Index) showed an overall trend of increasing from lactation to the finishing stage (P < 0.01). Gradual and significant changes in community structures were also observed along the four growth stages (ANOSIM, R = 0.66; P < 0.01). Non-parametric permutational multivariate analysis of variance shows that main factors driving the lifelong community dynamics included age and diet. Seventeen phylum members were discovered in the lifelong pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant phyla. LEfSe analysis revealed 63 bacterial features that are stage specific. By using a regressing tree based Random Forest model we identified five bacterial features that are associated with swine growth performance including features 26 (Turicibacteraceae Turicibacter), 27 (Clostridium butyricum), 18 (Clostridiaceae), 19 (Clostridium perfringens) and 4 (Clostridiaceae). Characterization of the lifelong dynamics of 17 healthy pigs from birth to market provides a foundation for gut microbiome studies focusing on swine development, health and growth performance.