Browsing by Author "Galyean, Michael L. (TTU)"
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Item A practical method to account for outliers in simple linear regression using the median of slopes(2024) Tedeschi, Luis O.; Galyean, Michael L. (TTU)The ordinary least squares (OLS) can be affected by errors associated with heteroscedasticity and outliers, and extreme points can influence the regression parameters. Methods based on the median rather than on the mean and variance are more resistant to outliers and extreme points. These methods could be used to obtain regression parameter estimates that reflect more accurately the genuine relationship between the Y and X variables, leading to better identification of outliers and extreme points by comparing the slopes and intercepts of both methods. The Theil-Sen (TS) regression computes all possible pairwise slopes and determines the median of slopes as the regression slope. Here, we illustrated the potential use of TS and frequently used robust regression (RR) techniques to single linear regression using synthetic datasets and a practical problem in animal science. Three synthetic datasets were created assuming the normal distribution of Y and X values: one was free of outliers, while the other two had one or two clusters of outliers but the same X values. The TS, OLS, and RR had nearly identical regression parameter estimates for the dataset without synthetic outliers. However, the intercept and slope estimates by the OLS method differed considerably from the TS and RR methods when one or two clusters of outliers were included. The TS approach could be used to indirectly determine the presence of outliers or extreme points by comparing the 95 % confidence interval of the TS and OLS parameter estimates.Item Feeding Management Strategies to Mitigate Methane and Improve Production Efficiency in Feedlot Cattle(2023) Galyean, Michael L. (TTU); Hales, Kristin E. (TTU)Mitigation of greenhouse gases and decreasing nutrient excretion have become increasingly important goals for the beef cattle industry. Because feed intake is a major driver of enteric CH4 production and nutrient excretion, feeding management systems could be important mitigation tools. Programmed feeding uses net energy equations to determine the feed required to yield a specific rate of gain, whereas restricted feeding typically involves decreasing intake relative to the expected or observed ad libitum intake. In the context of growing/finishing systems typical of those in the United States and Western Canada, experimental results with programmed and restricted feeding have often shown decreased overall feed intake and increased gain efficiency relative to ad libitum feeding, but too much restriction can negatively affect harvest weight and associated carcass quality. Slick feed bunk management is a time-based restriction that limits day-to-day variation in feed deliveries, but the effects on intake and performance are not well defined. Simulations to estimate enteric CH4 emission and nitrogen excretion indicated that programmed feeding of a high-grain diet could appreciably decrease CH4 emissions and nitrogen excretion compared with traditional growing programs based on high-forage diets. For feedlot finishing, programming gain for a portion of the feeding period will decrease CH4 emission and N excretion only if cattle perform better than expected during the programmed phase or if compensatory growth occurs when cattle are transitioned to ad libitum feeding. Optimal approaches to implement programmed or restricted feeding that will yield increased efficiency should be the subject of future research in this area.Item Influence of wet distillers grains diets on beef cattle fecal bacterial community structure(2012) Rice, William C.; Galyean, Michael L. (TTU); Cox, Stephen B.; Dowd, Scot E.; Cole, N. AndyBackground: The high demand for ethanol in the U.S. has generated large stocks of wet distillers grains (DG), a byproduct from the manufacture of ethanol from corn and sorghum grains. Little is known, however, about the potential influence of dietary DG on fecal microbial community structure. A better understanding of the microbial population in beef cattle feces could be an important monitoring tool to facilitate goals of improving nutrient management, increasing animal growth performance and decreasing odors and/or shedding of pathogens. Five diets consisting of a traditional diet fed to finishing beef cattle in the Southern High Plains of Texas-CON (steam-flaked corn control with 0% DG), and four concentrations of DG in the dietary dry matter; 10 C (10% corn-based DG), 5S (5% sorghum-based DG), 10S (10% sorghum DG), and 15S (15% sorghum DG) were fed to steers at the Texas Tech University Burnett Animal Center. Diets were essentially isonitrogenous with a formulated crude protein value of 13.5%. Results: Fecal grab samples were obtained from 20 steers (n = 4 per diet) and the barcoded DNA pyrosequencing method was used to generate 127,530 16S operational taxonomic units (OTUs). A total of 24 phyla were observed, distributed amongst all beef cattle on all diets, revealing considerable animal to animal variation, however only six phyla (core set) were observed in all animals regardless of dietary treatment. The average abundance and range of abundance, respectively of the core phyla were as follows: Firmicutes (61%, 19 to 83%), Bacteroidetes (28%, 11 to 63%), Proteobacteria (3%, 0.34 to 17.5%), Tenericutes (0.15%, 0.0 to 0.35%), Nitrospirae (0.11%, 0.03 to 0.22%), and Fusobacteria (0.086%, 0.017 to 0.38%). Feeding DG-based diets resulted in significant shifts in the fecal microbial community structure compared with the traditional CON. Four low abundance phyla significantly responded to dietary treatments: Synergistetes (p = 0.01), WS3 (p = 0.054), Actinobacteria (p = 0.06), and Spirochaetes (p = 0.06). Conclusions: This is, to our knowledge, the first study using this method to survey the fecal microbiome of beef cattle fed various concentrations of wet DG. Comparison of our results with other cattle DNA sequencing studies of beef and dairy cattle feces from a variety of geographical locations and different management practices identifies a core set of three phyla shared across all cattle. These three phyla, in order of relative abundance are; Firmicutes, Bacteroidetes, and Proteobacteria. The presence of large animal-to-animal variation in cattle microbiome was noted in our study as well as by others. © 2012 Rice et al; BioMed Central Ltd.Item Predicting metabolizable energy from digestible energy for growing and finishing beef cattle and relationships to the prediction of methane(2022) Hales, Kristin E. (TTU); Coppin, Carley A. (TTU); Smith, Zachary K.; McDaniel, Zach S. (TTU); Tedeschi, Luis O.; Cole, N. Andy; Galyean, Michael L. (TTU)Reliable predictions of metabolizable energy (ME) from digestible energy (DE) are necessary to prescribe nutrient requirements of beef cattle accurately. A previously developed database that included 87 treatment means from 23 respiration calorimetry studies has been updated to evaluate the efficiency of converting DE to ME by adding 47 treatment means from 11 additional studies. Diets were fed to growing-finishing cattle under individual feeding conditions. A citation-adjusted linear regression equation was developed where dietary ME concentration (Mcal/kg of dry matter [DM]) was the dependent variable and dietary DE concentration (Mcal/kg) was the independent variable: ME = 1.0001 × DE - 0.3926; r2 = 0.99, root mean square prediction error [RMSPE] = 0.04, and P < 0.01 for the intercept and slope. The slope did not differ from unity (95% CI = 0.936 to 1.065); therefore, the intercept (95% CI = -0.567 to -0.218) defines the value of ME predicted from DE. For practical use, we recommend ME = DE - 0.39. Based on the relationship between DE and ME, we calculated the citation-adjusted loss of methane, which yielded a value of 0.2433 Mcal/kg of dry matter intake (DMI; SE = 0.0134). This value was also adjusted for the effects of DMI above maintenance, yielding a citation-adjusted relationship: CH4, Mcal/kg = 0.3344 - 0.05639 × multiple of maintenance; r2 = 0.536, RMSPE = 0.0245, and P < 0.01 for the intercept and slope. Both the 0.2433 value and the result of the intake-adjusted equation can be multiplied by DMI to yield an estimate of methane production. These two approaches were evaluated using a second, independent database comprising 129 data points from 29 published studies. Four equations in the literature that used DMI or intake energy to predict methane production also were evaluated with the second database. The mean bias was substantially greater for the two new equations, but slope bias was substantially less than noted for the other DMI-based equations. Our results suggest that ME for growing and finishing cattle can be predicted from DE across a wide range of diets, cattle types, and intake levels by simply subtracting a constant from DE. Mean bias associated with our two new methane emission equations suggests that further research is needed to determine whether coefficients to predict methane from DMI could be developed for specific diet types, levels of DMI relative to body weight, or other variables that affect the emission of methane.Item Prediction of methane per unit of dry matter intake in growing and finishing cattle from the ratio of dietary concentrations of starch to neutral detergent fiber alone or in combination with dietary concentration of ether extract(2022) Galyean, Michael L. (TTU); Hales, Kristin E. (TTU)Previous research demonstrated that a fixed value of 0.2433 (SE = 0.0134) Mcal of CH4/kg of dry matter intake (DMI) could be used to predict CH4 production with accuracy and precision on par with similar equations in the literature. Slope bias was substantially less for the fixed-coefficient equation than noted for the other DMI- or gross energy intake (GEI)-based equations, but mean bias was substantially greater, presumably reflecting the failure of the fixed-coefficient approach to account for dietary factors that affect CH4 production. In this article, we report on the use of the dietary ratio of concentrations of starch to neutral detergent fiber (NDF) and dietary ether extract (EE) concentration to improve the accuracy and precision of the fixed-coefficient equation. The same development data set used to create the fixed-coefficient equation was used in the present study, which included 134 treatment means from 34 respiration calorimetry studies. Based on stepwise regression with dietary NDF, starch, crude protein, EE, and the starch:NDF ratio as possible dependent variables, the starch:NDF ratio and EE were the only dietary variables selected (P ≤ 0.15). The study-adjusted relationship with the starch:NDF ratio (r2 = 0.673; root mean square error [RMSE] = 0.0327) was: Mcal of CH4/kg of DMI = 0.2883 − 0.03474 × starch:NDF; whereas the relationship with a model that included both starch:NDF ratio and dietary EE (r2 = 0.738; RMSE = 0.0315) was: Mcal of CH4/kg of DMI = 0.3227 − 0.0334 × starch:NDF − 0.00868 × % EE. A previously published independent data set with 129 treatment means from 30 respiration calorimetry studies was used to evaluate these two equations, along with two additional equations in which g/d of CH4 was predicted directly from DMI, starch:NDF ratio, and/or dietary EE. The two Mcal of CH4/kg of DMI equations had superior fit statistics to the previously published 0.2433 Mcal of CH4/kg of DMI equation, with a substantial decrease in mean bias and improved concordance correlation coefficients. Moreover, the Mcal of CH4/kg of DMI equations resulted in improved fit relative to direct prediction of g/d of CH4 from DMI, the starch:NDF ratio, and % EE. Based on these results, further evaluation of the dietary ratio of starch-to-NDF concentrations and EE concentration to predict methane production per unit DMI in beef cattle is warranted.Item The future of beef production in North America(2011) Galyean, Michael L. (TTU); Ponce, Christian (TTU); Schutz, Jennifer (TTU)• North America accounts for more than one-quarter of the world's beef supply. Production per animal is highly efficient, particularly in the United States and Canada, but aspects of the long-term economic and environmental sustainability of the system need critical review. • Production units, especially concentrated systems like feedlots, face substantial regulatory pressure related to air and water quality, food safety issues, and animal welfare/animal rights issues. These pressures will increase in the future, as will concerns about effects of beef production on greenhouse gas emissions. • Public concerns for food safety will focus greater attention on animal traceability and liability associated with foodborne pathogens. Animal rights activism and consumer perceptions about "factory farming" production methods will challenge the use of concentrated feeding operations and pharmacological technologies in North American beef production systems. • Animal protein sources should play an important role in meeting global food demands, but to benefit from this demand, North American beef producers must produce safe, wholesome products, while placing greater emphasis on environmentally sound practices that maintain the highest standards for animal well-being.Item Validation of an experimental model to induce liver abscesses in Holstein steers using an acidotic diet challenge and intraruminal bacterial inoculation*†(2024) McDaniel, Zach S. (TTU); Hales, Kristin E. (TTU); Nagaraja, T. G.; Lawrence, Ty E.; Tennant, Travis C.; Amachawadi, Raghavendra G.; Carroll, Jeff A.; Burdick Sanchez, Nicole C.; Galyean, Michael L. (TTU); Davis, Emily (TTU); Kohl, Kesley (TTU); Line, Dalton J. (TTU); Dornbach, Colten W. (TTU); Abbasi, Mina; Deters, Alyssa; Shi, Xiaorong; Ballou, Michael A. (TTU); Machado, Vinicius S. (TTU); Smock, Taylor M. (TTU); Broadway, Paul R.Objective: Our objectives were to develop and evaluate a model to induce liver abscesses (LA) in cattle and assess roles of Fusobacterium and Salmonella on LA formation and severity. Materials and Methods: Holstein steers (n = 40; initial BW = 110 ± 12.0 kg) were assigned randomly to treatments (n = 10 per treatment): (1) control diet (CON); (2) acidotic diet (AD); (3) AD plus inoculation of Fusobacterium necrophorum ssp. necrophorum (8.81 × 1010 cfu/steer; ADFn); or (4) AD and intraruminal inoculation of F. necrophorum (8.81 × 1010 cfu/steer) and Salmonella enterica Lubbock (1.52 × 1011 cfu/steer; ADFS). On d 0, steers were subjected to 4 acidotic cycles where they were fed the acidotic diet for 3 d and then the control diet for 2 d. Intraruminal bacterial inoculation was on d 20. From d 21, AD, ADFn, and ADFS steers remained on the acidotic diet until d 38. Euthanasia occurred on d 38, and gross pathology of the lung, rumen, liver, and colon were recorded. Results and Discussion: Liver abscess prevalence was 40% in ADFn and 50% in ADFS versus 0% in CON and AD. No pathological differences were noted in lung nor colon among treatments; however, ruminal damage was more severe in ADFn and ADFS than in CON and AD steers. Implications and Applications: Acidotic diet alone caused mild ruminal acidosis but no LA. Acidotic diet with intraruminal bacterial inoculation increased rumenitis severity and resulted in LA, thus validating the nutritional model to induce LA. Therefore, acidotic diet with intraruminal bacterial inoculation is a viable model to study the formation of LA.