bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation Sequencing
Authors: Cheng Yu-Wei , Meyer Anders , Jakubowski Maureen A , Keenan Sean O , Brock Jay E , Azzato Elizabeth M , Weindel Michael , Farkas Daniel H , Rubin Brian P 
Published: December 2020

Abstract

Background
Methods for identifying gene fusion events, such as fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and transcriptome analysis, are either single gene approaches or require bioinformatics expertise not generally available in clinical laboratories. We analytically validated a customized next-generation sequencing (NGS) panel targeting fusion events in 34 genes involving soft-tissue sarcomas.

Methods
Specimens included 87 formalin-fixed paraffin-embedded (FFPE) tissues with known gene fusion status. Isolated total nucleic acid was used to identify fusion events at the RNA level. The potential fusions were targeted by gene-specific primers, followed by primer extension and nested PCR to enrich for fusion candidates with subsequent bioinformatics analysis.

Results
The study generated results using the following quality metrics for fusion detection: (a) ≥100 ng total nucleic acid, (b) RNA average unique start sites per gene-specific primer control ≥10, (c) quantitative PCR assessing input RNA quality had a crossing point &lt;30, (d) total RNA percentage ≥30%, and (e) total sequencing fragments ≥500 000.

Conclusions
The test validation study demonstrated analytical sensitivity of 98.7% and analytical specificity of 90.0%. The NGS-based panel generated highly concordant results compared to alternative testing methods.
213 Distribution of subjectively evaluated conformation traits in commercial growing replacement gilts
Authors: Moeller Grace A , Abell Courtney L , Somrack Tom P , Herring William O , Holl Justin W , Stalder Kenneth J 
Published: November 2020

Abstract
Feet and leg/locomotor issues represent a primary reason for sow removal from U.S. breeding herds. A shift from gestation stalls (GS) to group-sow housing (GSH) is occurring the U.S. swine industry, emphasizing the importance of structural soundness in replacement gilts. The objectives of this study were 1) to determine if feet and leg/body conformation score differences exist when evaluated at approximately 50 kgs. and 100 kgs.; 2) estimate subjectively scored feet and leg/body conformation trait repeatability within and across measurement time and scorer(s); and 3) determine if the ideal feet and leg conformation traits and scores within traits are the same within GS and GSH. A total of 4494 gilts were evaluated at approximately 22 weeks of age at 3 different farms within the same production system by 4 scorers, representing varying levels of experience. The conformation traits evaluated included locomotion score (LS), front and rear leg conformation (FLC and RLC), front and rear pastern angle (FP and RP), front and rear foot position (FFP and RFP), rib shape (RS), foot size (FS) and toe size (TS). Across farms, the mean gilt BW was 83 ± 11.5 kg. Across scorers and the entire gilt population, the mean conformation scores were: LS (0.06 ± 0.16), FLC (6.1 ± 0.54), RLC (5.4 ± 0.40), FP (3.6 ± 0.62), RP (4.0 ± 0.64), FFP (4.4 ± 0.31), RFP (4.1 ± 0.30), RS (4.3 ± 0.72), FS (2.0 ± 0.35) and TS (4.8 ± 0.61). The entire gilt population was divided amongst four individual sow herds (2 GS and 2 GSH). Sow performance will be followed for three parities to determine the relationship between production and longevity within gestation housing systems and determine if the relationships are associated with one or more conformation traits and/or differences in scores within each conformation trait.
195 Nutritional Influences on Brain and Cognitive Development
Authors: Dilger Ryan N 
Published: November 2020

Abstract
Nutrient ingestion during the prenatal and early-postnatal periods has profound effects on the developing brain and serves to shape the behaviors of young pigs. The pig is a versatile animal model for research in both the agriculture and human clinical realms, largely based on similarities in patterns of structural brain development between these species. Validated and sensitive neuroimaging techniques and assays for testing specific behaviors exist for the pig. While these readouts refer to cognitive performance indicators in the human context, the same behavioral measurements may refer to welfare states in animal agriculture. Recent nutrition studies, including those involving interactions with the intestinal microbiota, confirm the importance of early-life ingestion of iron, choline, milk-derived components, and even non-digestible fiber sources in shaping pig brain development and behaviors. Importantly, dietary patterns of the young pig can either support or hinder brain development and associated behaviors relative to age-matched controls. There are many advantages to translating evidence from pediatric nutrition research to animal agriculture by integrating outcomes related to the microbiota, gut-brain axis, and processes associated with cognitive function and brain development. Thus, studying the relationship between nutrition and neurodevelopment should be considered as an essential part of swine production.
38 Effects of combining nose flap weaning with short-term creep feeding of beef calves on cow and calf performance
Authors: Tjardes Kendi , Lippolis Katy 
Published: November 2020

Abstract
One hundred four Angus calves were ranked by gender, BW, age, and dam parity, and assigned to 1 of 4 pre-weaning treatments: 1) nose flaps for 7-d prior to weaning (NF), 2) traditional weaning (TRAD), 3) traditional weaning and creep feed for 3-wk prior to weaning (TRADC), or 4) nose flaps for 7-d prior to weaning and creep feed for 3-wk prior to weaning (NFC). Cow-calf pairs were housed in dry lot pens on d -28. From d -21 to 0, calves in creep treatments were provided free choice access to creep feed. Nose flaps were placed on d -7, and calves were weaned on d 0. Calves were vaccinated and dewormed on d -21 and 0. There was no difference (P ≥ 0.97) in calf BW on d -28 or -21. During the 7-d period that nose flaps were placed, NFC calves had greater (P ≤ 0.0001) ADG than NF and TRAD calves, and tended to have greater (P ≤ 0.10) ADG than TRADC calves. At weaning on d 0, TRADC and NFC calves tended to have greater BW (P = 0.07) and had greater overall change in BW (P &lt; 0.0001) during the pre-weaning period than TRAD and NF calves. Additionally, there was a greater (P ≤ 0.001) increase in BW of NFC and TRADC cows during the pre-weaning period compared to NF and TRAD cows. From d -21 to 0 there was no differences (P &gt; 0.41) in plasma concentrations for Bovine Viral Diarrhea Virus (BVD). By d 14, the TRADC calves had the greatest plasma concentrations for BVD (P &lt; 0.04). Therefore, providing short-term creep feed prior to placing nose flaps can improve pre-weaning calf and cow performance compared to traditional and nose flap weaning without creep feed supplementation, however, did not improve response to vaccination.
168 Nursery diets formulated with deoxynivalenol-contaminated corn reduced growth performance but did not modulate the cutaneous hypersensitivity response to ovalbumin or candida albicans
Authors: Lariviere Elise Lafleur , Zhu Cuilan , Zettell Sabrina , Patterson Rob , Huber Lee-Anne 
Published: November 2020

Abstract
A total of 144 newly weaned pigs (21 days of age) were used to determine the effect of deoxynivalenol (DON)-contaminated corn, with or without NutraMix™ supplementation, on growth performance and indices of immune system functionality during the nursery period. Pigs were randomly allocated to 24 pens of six pigs and assigned to 1 of 4 dietary treatments according to a 2X2 factorial design (n=6); treatments were fed for the 43±1-day nursery period in three phases (phases I, II, and III fed for 8, 14, and 21±1 days, respectively). The factors were clean or DON-contaminated corn and with (2 g/kg in complete diet) or without NutraMix™ supplementation. The DON diets were formulated to ensure a step-up in DON concentration for each phase (3, 4, and 5 ppm in phases I, II, and III, respectively; analyzed concentrations were 3, 3 and 4 ppm). Individual pig body weights and per pen feed intake were recorded weekly. Two pigs per pen were vaccinated against ovalbumin and candida albicans to measure humoral and cell-mediated immune responses by the cutaneous hypersensitivity response test. The ADG (600 vs 693±28 g) and ADFI (979 vs 1110±51 g) in phase III and final BW (25.2 vs 27.1±0.9 kg) were reduced for pigs fed contaminated corn (P&lt; 0.005, P=0.088, and P&lt; 0.05, respectively). NutraMix™ supplementation tended (P=0.086) to improve ADFI (181 vs 142±14 g) in the first week after weaning. All pigs responded to both ovalbumin and candida albicans during the cutaneous hypersensitivity response (P&lt; 0.05), but DON nor NutraMix™ influenced the response. The DON-contaminated diets had the greatest impact on pig growth performance during phase III and when DON concentration was 4 ppm, with no modulation of the cutaneous hypersensitivity response. NutraMix™ supplementation during the early weaning period may be a means to stimulate nursery pig feed intake.
202 Determining the effects of increasing dietary standardized ileal digestible lysine levels on growth performance and carcass characteristics of growing-finishing pigs from 29- to 129-kg
Authors: Kitt Steve J , Cast Wayne , Hover Mark , Vier Carine , Sievers Chris , Lu Ning , Betlach Alyssa , Hamilton Dan , Kiehne Ross , Orlando Uislei 
Published: November 2020

Abstract
Our objective was to determine the effects of increasing standardized ileal digestible (SID) lysine (Lys) levels on growth performance and carcass characteristics of growing-finishing pigs. A total of 1,013 barrows and gilts (PIC337×Camborough, initially 29.2±0.21 kg) were used in a 112-d growth trial with 25 or 26 pigs per pen and 13 pens per treatment in a randomized complete block design. Diets were corn-soybean meal (SBM)-dried distillers grains with solubles-based, and treatments were achieved through the inclusion of SBM at the expense of corn. Diets were fed in 6 phases and formulated to be iso-caloric within each phase. Treatments consisted of: 1) Low Lys: overall dietary SID Lys levels as 87% of PIC2016 Lys requirement; 2) Medium Lys: overall dietary SID Lys levels as 97% of PIC2016 Lys requirement; 3) High Lys: overall dietary SID Lys levels as 106% of PIC2016 Lys requirement. Experimental data were analyzed using generalized linear mixed models with pen as the experimental unit. Pigs fed High or Medium Lys had greater (P&lt; 0.01) average daily gain compared to pigs fed Low Lys. There was no evidence (P &gt;0.10) for the difference between treatments for average daily feed intake. Pigs fed High Lys had the greatest (P&lt; 0.01) feed efficiency (G:F) followed by Medium Lys, with pigs fed Low Lys with the lowest G:F. Pigs fed High or Medium Lys had greater (P&lt; 0.01) hot carcass weight, loin depth, and lean percentage compared to pigs fed Low Lys. There was no evidence (P &gt;0.10) for treatment effect on carcass yield and backfat. Pigs fed Low Lys had greater removal and mortality rate than those fed High or Medium Lys (P&lt; 0.01). In conclusion, increasing SID Lys over PIC2016 recommendations through increasing SBM levels resulted in increased growth performance and carcass characteristics, and reduced removal and mortality rate of 29- to- 129 kg pigs.
177 Effect of supplementing a fatty acid-based product, Monomix, or pharmacological levels of zinc oxide on growth performance of nursery pigs
Authors: Batson Kelsey L , Thomas Lori , Woodworth Jason C , Tokach Mike D , Goodband Robert D , Dritz Steve S , DeRouchey Joel M , Bryte Jim 
Published: November 2020

Abstract
Trials suggest short and medium chain fatty acids can be used as alternatives for ZnO; however, US studies are limited. Therefore, the objective of this study was to evaluate the effects of a short and medium chain fatty acid product (Monomix, Quality Technology International, Inc., Elgin, IL) added alone or in combination with pharmacological levels of ZnO on nursery pig performance. A total of 354 pigs (DNA 200×400, initial BW=5.9 kg) were randomized to pens (5 pigs/pen) and pens were allotted to 1 of 4 treatments with 18 replicates/treatment. Treatments were arranged in a 2×2 factorial with main effects of added ZnO (0 vs. 3,000/2,000/0 ppm of Zn in phases 1, 2, and 3 respectively) and Monomix (0 vs. 0.4% in phases 1, 2, and 3). Treatment diets were formulated in three phases fed from d 0 to 7, 7 to 18, and 18 to 35 post-weaning with all diets containing 110 ppm Zn from the trace mineral premix. Data were analyzed as completely randomized design using the PROC GLIMMIX procedure of SAS with pen as the experimental unit. No ZnO × Monomix interactions (P=0.399) were observed. Feeding Monomix decreased ADFI (P=0.002) and ADG (P=0.012) from d 0 to 7, resulting in decreased d 7 BW (P=0.015) but there was no evidence for other differences. Feeding ZnO from d 0 to 7 and 7 to 18,increased ADG (P&lt; 0.001), ADFI, and BW, and improved G:F. Overall from d 0 to 35, pigs fed diets with added ZnO in phases 1 and 2 had increased (P&lt; 0.05) ADG, ADFI, and d 35 BW, with no evidence for differences in performance in pigs fed diets with Monomix. The addition of Monomix failed to improve pig performance, whereas pharmacological levels of ZnO improved ADG and ADFI.
284 Effect of formulating diets based on a ratio between STTD Ca and STTD P and the inclusion of phytase on growth performance, plasma Ca and P, and bone ash of pigs from 11 to 130 kg
Authors: Lagos Vanessa , Bedford Mike R , Stein Hans H 
Published: November 2020

Abstract
A 126-d experiment was conducted to test the hypothesis that the requirement for Ca expressed as a ratio between standardized total tract digestible (STTD) Ca and STTD P obtained in short-term experiments may be applied to pigs fed diets without or with microbial phytase from 11 to 130 kg. In a 5-phase program, 160 pigs (11.2 ± 1.8 kg) were randomly allotted to 32 pens and 4 corn-soybean meal diets in a 2 × 2 factorial design with 2 formulation strategies (total Ca or STTD Ca), and 2 phytase levels (0 or 500 units/kg) assuming phytase released 0.11% STTD P and 0.16% total Ca. The STTD Ca:STTD P ratios were 1.40:1, 1.35:1, 1.25:1, 1.18:1, and 1.10:1 for phases 1 to 5. At the conclusion of each phase, weights of pigs and feed left in feeders were recorded and a blood sample from 1 pig per pen was collected. At the end of phases 1 (d 24) and 5, the right femur of 1 pig per pen was collected. Data were analyzed as main effects of formulation strategy and phytase level and their interaction. Phase effect was analyzed by repeated measures. No interactions were observed and formulation strategy and phytase did not impact growth performance, bone ash, or plasma Ca and P on d 24 (Table 1). On d 126, an interaction (P &lt; 0.05) between main effects was observed. Without phytase, pigs fed diets based on total Ca had greater bone ash than STTD Ca pigs, but with phytase, no differences were observed. A negative quadratic effect (P &lt; 0.05) of phase for plasma Ca and P was observed. In conclusion, STTD Ca:STTD P ratios can be used in diet formulation for growing-finishing pigs without affecting growth performance. Phytase ameliorates bone resorption caused by low Ca in STTD Ca diets.
102 Pooled analysis of six large-pen feedlot studies: Non-coated initial and a non-coated terminal implant compared with a single initial and delayed release implant at arrival in feedlot heifers
Authors: Smith Zachary K , Crawford Grant , Nichols Wade , Nuttelman Brandon , Streeter Marshall , Hutcheson John , Amrine David , Renter David 
Published: November 2020

Abstract
Randomized complete block design experiments (n = 6 experiments) were conducted in large-pen feedlot research facilities between 2015 and 2018 comparing an 80 mg trenbolone acetate (TBA) and 8 mg estradiol-17β (E2) initial implant and re-implant with 200 mg TBA and 20 mg E2 protocol (IH/200) to a single 80 mg TBA and 8 mg E2 uncoated; 120 mg TBA and 12 mg E2 coated implant at arrival (XH) on growth and carcass responses in finishing heifers. Experiments occurred in Nebraska, Oklahoma, Washington, and Texas. Similar arrival processing was used across experiments where 17,675 heifers [initial BW = 333 kg SEM (4.1)] were enrolled into 180 pens (90 pens/treatment with 65 to 240 heifers/pen) and fed for 152 to 214 d. Only IH/200 heifers were removed from their pen at re-implant. Diets contained monensin and tylosin, consisted of ingredients common to each region, and contained greater than 90% concentrate. Ractopamine hydrochloride was fed for a minimum of 28 d prior to harvest. Linear mixed-models were used for all analyses; model-adjusted means for each implant group and the corresponding SEM were generated. Distributions of USDA quality (QG) and yield grade (YG) were analyzed for ordinal outcomes. No differences (P ≥ 0.11) were detected for any performance parameters except DMI, where XH had greater (P = 0.02) DMI (9.48 vs. 9.38 ± 0.127 kg) compared with IH/200. Heifers implanted with IH/200 had greater (P ≤ 0.02) HCW by 1.3%, caused by greater dressing percentage, and ribeye area; lesser (P ≤ 0.01) back fat by and calculated YG, while marbling scores were similar (P = 0.74) compared with XH heifers. Distributions of USDA YG and QG were impacted (P ≤ 0.03) by treatment, IH/200 had fewer USDA Prime and YG 4 and 5 carcasses. These data indicate that heifer growth performance did not differ between implants, but HCW and muscling did; IH/200 is suited for grid marketing and XH is suited for heifers sold on a live basis.
228 Effect of exogenous glucoamylase inclusion on in vitro digestion and feedlot cattle performance
Authors: Pittaluga Alejandro , Yu Shukun , Li Wenting , McCann Joshua C 
Published: November 2020

Abstract
The objective was to evaluate the effect of adding an exogenous glucoamylase (GA) enzyme to a finishing diet on in vitro digestion and performance of feedlot cattle. Experiment 1 evaluated 3 levels of added enzyme (0, 0.24, and 0.72 GA enzyme units) and 2 corn particle sizes (2 and 4 mm) in a 7 h in vitro batch culture fermentation. No interactions were observed (P &gt; 0.10). Addition of GA increased (P &lt; 0.01) in vitro dry matter disappearance by 9%. A smaller corn particle increased (P &lt; 0.01) in vitro dry matter disappearance by 11%. In Experiment 2, Angus × Simmental steers (N = 105; BW = 340 ± 39 kg) were blocked by weight and assigned to 15 pens. Pens were randomly assigned to one of 3 treatments: control (CON) diet with no added enzymes, low inclusion of GA (122 enzyme units/kg DM; LGA), or high inclusion of GA (183 enzyme units/kg DM; HGA). Steers were fed a basal diet consisting of 60% dry rolled corn, 17.5% modified distillers grains with solubles, 12.5% corn silage, and 10% of a corn-based supplement on a DM basis for 139 d. Inclusion of GA did not affect (P ≥ 0.24) final BW, DMI, or ADG overall for the 136 d feeding period. Steers fed HGA had increased (P = 0.02) G:F compared with LGA and CON with least square means of 0.213, 0.194, and 0.197, respectively. Inclusion of GA did not affect (P ≥ 0.19) carcass traits including HCW, 12th rib fat thickness, yield grade, longissimus muscle area, or marbling score. Overall, results suggest inclusion of exogenous glucoamylase enzyme increased in vitro dry matter disappearance in batch culture and improved feed conversion of the finishing diet fed to feedlot steers at 0.381 g enzyme protein/kg DM.
227 Impact of feeding Aspergillus subspecies (ssp.) blend and different corn processing methods on finishing beef cattle performance and carcass characteristics
Authors: Hopfauf Stacia M , Boyd Bradley M , McPhillips Levi J , Erickson Galen E 
Published: November 2020

Abstract
The objective of this study was to evaluate the effect of feeding Aspergillus ssp. blend in combination with dry-rolled (DRC) or high-moisture corn (HMC) based finishing diets on performance and carcass characteristics. Crossbred beef steers (n = 320; initial BW = 267 ± 9 kg) were utilized in a generalized randomized block design. Cattle were assigned randomly to pens by initial body weight (BW) and pens were assigned randomly to one of four treatments with 8 pens per treatment for simple effect means. Treatments were set up as a 2 × 2 factorial arrangement with factors consisting of corn processing and 0 g / steer daily or 10 g / steer daily Aspergillus ssp. blend. There were no significant interactions (P ≥ 0.23) observed between corn processing and Aspergillus ssp. blend in the diet; therefore, only main effects are discussed. For the main effect of Aspergillus ssp. blend; no significant differences were observed for dry-matter intake (DMI), average daily gain (ADG), feed efficiency (G:F), hot carcass weight (HCW), or carcass traits (P ≥ 0.78). Cattle fed Aspergillus ssp. blend had a greater 12th rib fat (P = 0.05). For the main effect of corn processing, cattle fed DRC had heavier HCW and final BW (P = 0.04), greater ADG (P = 0.05), and greater DMI (P &lt; 0.01). However, steers fed HMC had greater G:F (P &lt; 0.01) compared to DRC. These data suggest that feeding Aspergillus ssp. blend in either with dry-rolled or high moisture corn diets did not significantly improve performance or carcass characteristics in finishing beef steers. While feeding HMC improved feed efficiency compared to DRC, feeding DRC increased ADG (and also DMI) compared to HMC.
294 Effects of bedding application on growth performance and carcass traits in finishing beef steers during the winter and spring in eastern South Dakota
Authors: Smerchek Dathan , Smith Zachary K 
Published: November 2020

Abstract
Two-hundred and forty Continental × English beef steers (allotment BW = 365 kg [SD 22.5]) were used in a randomized complete block design feedlot study to evaluate the effects of bedding application during the finishing phase. Steers were allotted to 30 concrete surface pens (n = 8 steers/pen) at the Ruminant Nutrition Center (RNC) in Brookings, SD. A common diet was fed that contained 2.09 Mcal/kg of NEm and 1.39 Mcal/kg of NEg and provided 30 g/ton of monensin sodium to diet DM. Pens were assigned to 1 of 2 treatments: 1) No bedding applied (NO) or 2) 1.8 kg (as-is basis) of wheat straw bedding/steer/d (BED). The first 9 pen replicates began on test 14 d prior to the last 6 pen replicates. Pen was the experimental unit; an α of 0.05 determined significance. This study was part of a factorial experiment that included steroidal implant. No interactions were detected (P ≥ 0.09). Daily ambient temperature (n = 183) averaged 4.33°C [SD 3.21] during the study. Dry matter intake was increased (P = 0.01) by 5.8% in BED compared to NO. Carcass-adjusted ADG (P = 0.01) and G:F (P = 0.01) were increased in BED by 21.0% and 14.4%, respectively. Carcass-adjusted final BW and HCW tended to differ (P ≤ 0.07) between NO and BED. Cattle from NO required an additional 35 days to achieve similar final live BW. Rib eye area (P = 0.69) did not differ between NO and BED. Dressing percentage (P = 0.01; 63.29 vs. 62.30 ± 0.410%), backfat (P = 0.01; 1.19 vs. 1.09 ± 0.410 cm), marbling (P = 0.01; 475 vs. 437 ± 6.6), and yield grade (P = 0.03; 2.95 vs. 2.81 ± 0.045) were increased in NO. Estimated metabolic rate was elevated (P = 0.02; 0.0995 vs. 0.0948 ± 0.013 Mcal/BW0.75, kg), for NO vs. BED. Bedding improved feedlot finishing phase growth performance and gain efficiency during finishing in eastern South Dakota.