Browsing by Author "Chapman, Phillip L., committee member"

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Open Access
An evaluation of the effectiveness of FreshCase® technology to extend the shelf life of beef and pork
(Colorado State University. Libraries, 2012) Yang, Xiang, author; Belk, Keith E., advisor; Woerner, Dale R., advisor; Chapman, Phillip L., committee member; Tatum, J. Daryl, committee member
This research evaluated the effect of FreshCase®, a novel packaging technology that has been shown to extend the shelf life of whole muscle beef and ground beef, whole muscle pork and ground pork sausages by stabilizing fresh meat color. FreshCase® utilizes a high-barrier nitrite containing film in conjunction with vacuum packaging technology. Storage life was defined by the number of days required to reach an aerobic psychrotrophic plate count of 107 log CFU/g, and all treatmes were stored and evaluated until storage life expired. The storage life for beef steaks stored in FreshCase® packages at 4°C was 36 days; and the shelf life for ground beef stored in FreshCase® packages at 4°C was 12 days. The shelf life for pork chops stored in FreshCase® packages at 1°C was 46 days; and the shelf life for ground pork sausages stored in FreshCase® packages at 1°C was 19 days. Values for CIE a* (redness) were greater (P < 0.05) for FreshCase®-packaged samples for both beef steaks and ground beef with the increase of storage time. Both pork chops and sausages stored in FreshCase® packages retained more acceptable redder color (P < 0.05) than those stored in Control packages throughout storage. By the point at which spoilage was detected, off-odors of putrid, acid, sour and rancidity for FreshCase®-packaged samples were detected, but were present at very low level. Likewise, by the point of spoilage, no significant differences (P > 0.05) were found between samples in control and FreshCase® packages in all off-odors detection for both pork chops and sausages and the intensities of these off-odors were very low. Also, beef and pork samples resulted in very low (1.19 mg malonaldehyde/kg and 0.55 mg malonaldehyde/kg, respectively) TBA values throughout storage. Therefore, utilization of FreshCase® Technology in whole muscle beef and ground beef, whole muscle pork and ground pork sausages results in a more stable fresh red meat color with a low level of off-odors, and lipid oxidation. FreshCase® did not influence microbial growth in vacuum packaged samples.
Open Access
Habitat estimation through synthesis of species presence/absence information and environmental covariate data
(Colorado State University. Libraries, 2011) Dornan, Grant J., author; Givens, Geof H., advisor; Hoeting, Jennifer A., committee member; Chapman, Phillip L., committee member; Myrick, Christopher A., committee member
This paper investigates the statistical model developed by Foster, et al. (2011) to estimate marine habitat maps based on environmental covariate data and species presence/absence information while treating habitat definition probabilistically. The model assumes that two sites belonging to the same habitat have approximately the same species presence probabilities, and thus both environmental data and species presence observations can help to distinguish habitats at locations across a study region. I develop a computational method to estimate the model parameters by maximum likelihood using a blocked non-linear Gauss-Seidel algorithm. The main part of my work is developing and conducting simulation studies to evaluate estimation performance and to study related questions including the impacts of sample size, model bias and model misspecification. Seven testing scenarios are developed including between 3 and 9 habitats, 15 and 40 species, and 150 and 400 sampling sites. Estimation performance is primarily evaluated through fitted habitat maps and is shown to be excellent for the seven example scenarios examined. Rates of successful habitat classification ranged from 0.92 to 0.98. I show that there is a roughly balanced tradeoff between increasing the number of sites and increasing the number of species for improving estimation performance. Standard model selection techniques are shown to work for selection of covariates, but selection of the number of habitats benefits from supplementing quantitative techniques with qualitative expert judgement. Although estimation of habitat boundaries is extremely good, the rate of probabilistic transition between habitats is shown to be difficult to estimate accurately. Future research should address this issue. An appendix to this thesis includes a comprehensive and annotated collection of R code developed during this project.
Open Access
Identifying preferences for specific beef flavor characteristics
(Colorado State University. Libraries, 2012) O'Quinn, Travis Gene, author; Belk, Keith E., advisor; Tatum, J. Daryl, advisor; Woerner, Dale R., committee member; Engle, Terry E., committee member; Chapman, Phillip L., committee member
Descriptive sensory analysis of beef samples was conducted at culinary institutions in three regions of the United States to determine differences in beef flavor attributes and flavor preferences among 12 different beef product categories (treatments). Treatments were chosen specifically to permit identification and characterization of production-related beef flavor differences, including effects of USDA grade (Prime, Premium Choice, Low Choice, Select), cattle breed-type (Angus, Holstein, American Wagyu), finishing diet (grass-fed, corn-fed, barley-fed), use of growth technologies (non-implanted, implanted, implanted & fed β agonists), and postmortem aging method (wet-aged, dry-aged). Panelists (N = 307) rated ground strip loin samples from each treatment for 13 different flavor notes (beefy/brothy, browned/grilled, buttery/beef fat, nutty/roasted nut, earthy/mushroom, bloody/metallic, grassy, livery, fishy, sour, sweet, and bitter) and overall flavor desirability. Each sensory attribute was rated on a 10-cm, unstructured line scale with 0 cm verbally anchored at very low intensity for all flavors and dislike extremely for flavor desirability and 10 cm verbally anchored at very high intensity for all flavors and like extremely for flavor desirability. In addition, samples were analyzed to determine percentage chemical lipid, moisture, protein, and ash of raw products, fatty acid composition of cooked products, and quantities of volatiles produced during cooking. Of the factors analyzed, USDA Quality grade and finishing diet (grain-fed vs grass-fed) had the largest effects on beef flavor attributes. Differences in cattle-breed type (Angus vs Wagyu), grain source (corn vs barley), aging technique (dry-aged vs wet-aged), and use of growth technology (non-implanted vs implanted vs implanted & fed β agonists) had only minimal effects on flavor. Extending the wet-aging period from 14 to 46 d had a negative effect on flavor, producing samples that scored higher (P < 0.05) for sour flavor than all other treatments. Panelists preferred samples with flavors described as beefy/brothy, browned/grilled, buttery/beef fat, nutty/nutty roasted nut, and sweet, and disliked flavors identified as bloody/metallic, grassy, gamey, livery, fishy, sour, and bitter. Moreover, overall flavor desirability scores were positively correlated (P < 0.05) with the concentration of several monounsatured fatty acids including C12:1, C14:1, C16:1 c9, and C18:1 c9. Stearic acid (C18:0) concentration was negatively correlated (P < 0.05) with overall flavor desirability and positively correlated (P < 0.05) with bloody/metallic, grassy/hay like, gamey, livery, fishy, sour, and bitter flavors. The concentration of several polyunsaturated fatty acids including C18:2t (total), C18:3 n-3, and C22:5 n-3, were found highest (P < 0.05) in Organic grass-fed samples and were negatively correlated (P < 0.05) with overall flavor desirability. Overall flavor desirability was positively correlated (P < 0.05) with diacetyl (2, 3-butanedione), acetoin (3-hydroxy-2-butanone), 3-methyl butanal, and pentanal concentrations. Samples with higher concentrations of dimethyl sulfide were rated lower (P < 0.05) for overall flavor desirability. The concentrations of several volatile compounds were correlated with various beef flavors including beefy/brothy, buttery/beef fat, browned/grilled, earthy/mushroom, nutty/roasted nut, sour, bitter, and sweet.
Open Access
Oropharyngeal bacteria, with respect to animal health classification, and viral serology of Montana bighorn sheep (Ovis canadensis) and domestic (Ovis aries) near to and distant from the wildlife/domestic animal interface
(Colorado State University. Libraries, 2010) Miller, David Steven, author; Campbell, Terry W., advisor; Garry, Franklyn, advisor; Chapman, Phillip L., committee member; Kimberling, Cleon V., committee member; Rhyan, Jack C., committee member
Respiratory disease outbreaks attributed to pasteurellosis have lead to conflict at the wildlife/domestic interface, where domestic sheep have been hypothesized to be a reservoir of Pasteuerellaceae strains that cause disease in bighorn sheep. This dissertation compares bighorn sheep ( Ovis canadensis) and domestic sheep ( O. aries) oropharyngeal Pasteurellaceae biovariants from animals classified as diseased and healthy. It also compares bacteriology and viral serology of populations of these species near to and distant from the wildlife/domestic livestock interface. A retrospective study of clinical submissions (1990 - 2004) indicated that 94 Pasteurellaceae biovariants have been associated with domestic sheep classified as diseased. A second retrospective study (1989 - 2004) indicated that 37 Pasteurellaceae biovariants have been associated with bighorn sheep classified as diseased. A prospective study of domestic and bighorn sheep near to and distant from the wildlife/domestic interface indicated that Pasteurellaceae biovariants commonly associated with disease in the retrospective studies were also common in healthy animals, and that there was extensive interspecific sharing of biovariants. This suggests that a simple agent/disease relationship may not exist for Pasteurellaceae in these host species. In addition, it is not clear that either species serves as a reservoir for Pasteurellaceae that are pathogenic for the sympatric species. However, unstated assumptions that single samples represent an animal's Pasteurellaceae microflora are questionable, based on the minimal concordance of biovariants of individual domestic livestock (n = 118) sampled six months apart. Based on the populations in the prospective study, bighorn sheep populations were naive to Mycoplasma, and both Ovis species were largely naive to infectious bovine rhinotracheitis and bovine virus diarrhea 1 and 2. This suggests that these agents may cause outbreaks if introduced into these populations. Cluster analysis of Pasteurellaceae and viral serology results identified four different clusters (P < 0.0001), but these did not closely correspond to species and location categories. The results from this study suggest that emphasis on single determinants for causes of respiratory disease outbreaks in domestic and bighorn sheep, rather than determination of risk factors for multiple determinants, may not provide results that are useful for managing disease in these species.
Open Access
Prediction of meat tenderness using high resolution imaging
(Colorado State University. Libraries, 2010) Howard, Scott Thomas, author; Belk, Keith Evan, 1961-, advisor; Tatum, J. Daryl, committee member; Chapman, Phillip L., committee member
Tenderness plays an important role in the sensory attributes of beef products. The objective of this study was to obtain the highest quality and resolution images of cross-sections of beef Longissimus dorsi surfaces that could likely be replicated in a commercial environment; and, to develop algorithms and regression equations that predict aged beef shear force. Fifty carcasses were identified at each of three commercial beef processing facilities in Colorado, Nebraska and Texas (total N = 150). A-maturity carcasses were selected to fill an equal distribution over the entire range of beef marbling scores; 1/3 of carcasses represented marbling scores from Practically Devoid 00 to Slight 40, 1/3 from Slight 50 to Small 90 and 1/3 from Modest 00 or higher. Carcasses derived from cattle supplemented with Zilpaterol hydrochloride (n = 25, based on harvest facility records) were identified as such. Samples were excised from the Longissimus muscle immediately posterior to the 12 th /13 th rib interface and imaged using the Tenera Technology High Resolution Imaging System; in addition, reflectance measurements (L*, a*, b*) were obtained. Samples were aged for either 7 or 14 days prior to freezing. Steaks were fabricated from frozen samples for Warner-Bratzler shear force (WBSF) determination. Images were analyzed using the custom developed Tenera Technology ZARMT software program, generating 10 output variables (diaSml, propSml, diaLrg, propLrg, ratDia, ratProp, medDia, medProp, diaNormMax and propNormMax) thought to represent ultra-structural characteristics of muscle such as fiber diameter, proportion of large versus small fibers and predominant size of muscle fiber within a given sample, which have previously been associated with beef tenderness (Hiner et al., 1953; Tuma et al., 1962; Herring et al., 1965; Cooper et al., 1968). In 14d aged steaks from harvest facility one, the use of high resolution variables explained an additional 11% of the variation in WBSF value over the use of marbling and color variables alone. Within harvest facility two and three, high resolution variables allowed for explanation of an additional 25% and 17% of the variation in 14d WBSF respectively. For samples aged 7d, high resolution variables allowed for explanation of an additional 8%, 14% and 34% of the variation in WBSF values of steaks from harvest facility one, two and three respectively. Fourteen days postmortem, inclusion of high resolution variables improved classification of "tender" steaks (WBSF less than or equal to 3.7, Platter et al., 2003a) 40%, -3% and 7% from harvest facility one, two and three respectively. Classification of "tough" steaks (WBSF greater than 3.7, Platter et al., 2003a) within steaks aged 14d was improved by -10%, 0% and 0% through use of high resolution variables. In classification of "tough" versus "tender" steaks 7d postmortem, equations containing high resolution variables correctly classified an additional 6%, 14.3% and 7.1% of "tender" steaks and 0%, -5.9% and 9.1% of "tough" steaks from harvest facility one, two and three respectively. Compared with the use of marbling and reflectance measurements alone, the use of high resolution variables improved the ability to explain WBSF at 7d and 14d, as well as in the designation of "tough" and "tender" steaks/carcasses, suggesting this technology, or one measuring similar traits could improve the assurance of tender beef products at the consumer level.
Open Access
Prediction of primal and subprimal beef yields with video image analysis
(Colorado State University. Libraries, 2011) Nunes, Trevor Francis, author; Belk, Keith Evan, 1961-, advisor; Tatum, J. Daryl, committee member; Smith, Gary C., committee member; Chapman, Phillip L., committee member
An ability to segregate carcasses based on both primal and subprimal yields would further facilitate value-based marketing in the beef industry. This study was conducted to evaluate Video Image Analysis (VIA) output to predict fabricated primal and subprimal yields. Carcasses were selected based on yield grade (YG 1, YG 2, YG 3, YG 4, and YG 5) as well as hot carcass weight (< 341 kg and ≥ 341 kg). A yield dissection was performed and at each step in fabrication, recovered product weights for each carcass to remain in the study summed to ≥ 99 % of the starting chilled weight of each primal and subprimal. For yield predictions, VIA output from 12th/13th rib interface images from the VBG 2000 (single-component; n = 142, development; n = 58, validation), or from VBG 2000 output in combination with output from loin/round primal interface images from the VPS 2000 (dual-component; n = 129, development; n = 56, validation) were regressed on yields of fabricated primals and subprimals. Yield variables were predicted as a percent of the aggregate chilled carcass side weight. Results from prediction equations for primals or the largest subprimal representing a primal in the study, indicated moderate and low predictive capability for development and validation datasets, respectively. For the square cut chuck (IMPS 113), commodity iii trimmed brisket (IMPS120, PS0 1), ribeye (IMPS 112A, PSO 3, 5.1 cm x 5.1 cm lip-on), short plate (IMPS 121), loin primal (IMPS 172), flank primal, and round primal (IMPS 158) R2 / adjusted R2 values (development / validation) of 0.39 / 0.11, 0.16 / 0.05, 0.31 / 0.12, 0.40 / 0.03, 0.56 / 0.12, 0.35 / -.005, and 0.64 / -0.05, respectively, for single-component predictions and 0.60 / -0.13, 0.57 / -0.03, 0.40 / 0.08, 0.52 / -0.15, 0.66 / -3.42, 0.66 / -3.42, 0.47 / -0.004, and 0.73 / -0.10, respectively, for dual-component predictions was observed. The best performing single-component model was for the tenderloin (IMPS 189A) with R2 / adjusted R2 values (development / validation) of 0.42 / 0.50. The best performing dual component model was for the cap off inside round (IMPS 169A) with R2 values (development / validation) of 0.58 / 0.30. The ability of single-component and dual-component equations to predict yields of several primal and subprimal cuts, with reasonable accuracy and precision in the development dataset, yet low accuracy and precision in the validation dataset, suggests that the VIA systems tested in this study do not have the potential as tool for more sensitive carcass segregation at this time. Further investigation to reveal the full potential of dual-component primal and subprimal cut yield prediction, perhaps looking at a sample population with greater variance (i.e., equal number of yield grades for equation development) and having VPS 2000 images available from each primal surface to provide independent variables representative of the entire carcass, is justifiable.
Open Access
Quantifying the "aging response" and nutrient composition for muscles of the beef round
(Colorado State University. Libraries, 2010) Dixon, Cheyenne Lee, author; Belk, Keith E., advisor; Chapman, Phillip L., committee member; Tatum, J. Daryl, committee member; Woerner, Dale R., committee member
The objective of this study was to determine the optimal postmortem aging period and nutrient composition for Beef Value Cuts of the round. For the postmortem aging study, 40 USDA Select and 40 premium USDA Choice beef carcasses were selected from a commercial beef packing plant in Colorado over a 12-week period. The bottom and inside rounds were collected from both sides of each carcass for further fabrication into the following muscles: Adductor, Gastrocnemius, Gracilis, Pectineus, and Superficial digital flexor. Each pair of muscles was cut into seven steaks, approximately 2.54 cm in thickness, and vacuum packaged. All steaks were randomly assigned to one of the following aging periods: 2, 4, 6, 10, 14, 21, and 28 days, and placed in refrigerated storage (2°C, never frozen). Upon completion of the designated aging period, steaks were removed from storage, cooked to a peak internal temperature of 72°C, and evaluated using Warner-Bratzler shear force (WBSF). A two-way interaction was detected (P < 0.05) between individual muscle and postmortem aging period. The WBSF of all muscles except the Superficial digital flexor decreased with increased time of postmortem aging. Quality grade did not affect (P > 0.05) WBSF values for the Adductor, Gastrocnemius, Pectineus, and Superficial digital flexor muscles. Exponential decay models were used to predict the change in WBSF from 2 to 28 days postmortem (aging response). The Adductor, Gastrocnemius, Select Gracilis, premium Choice Gracilis, and Pectineus required 21, 14, 23, 23, and 25 days, respectively, to complete the majority of the aging response. To determine the nutrient composition of the Adductor, Gastrocnemius, Gracilis, Pectineus, Semimembranosus, and Superficial digital flexor, bottom and inside rounds were collected from 10 USDA Select and 10 premium USDA Choice carcasses, fabricated into the respective muscles, cut into 2.54 cm cubes, frozen (-20°C), and then homogenized. The Adductor, Gracilis, Pectineus, Semimembranosus, and Superficial digital flexor were analyzed for dry matter, moisture, crude protein, and ash percentages. All muscles were evaluated for lipid percentage and fatty acid and cholesterol composition. When quality grades were combined, all muscles fell into the "extra lean" or "lean" categories specified by USDA guidelines based on the total fat, saturated fat, and cholesterol content present in each cut. Results of this study illustrate the potential for Beef Value Cuts of the round to be sold in foodservice operations and retail stores with marketing emphasis being placed on the exceptional leanness and acceptable tenderness of these cuts.
Open Access
Saddlepoint approximation to functional equations in queueing theory and insurance mathematics
(Colorado State University. Libraries, 2010) Chung, Sunghoon, author; Butler, Ronald W., advisor; Scharf, Louis L., committee member; Chapman, Phillip L., committee member; Hoeting, Jennifer A. (Jennifer Ann), 1966-, committee member
We study the application of saddlepoint approximations to statistical inference when the moment generating function (MGF) of the distribution of interest is an explicit or an implicit function of the MGF of another random variable which is assumed to be observed. In other words, let W (s) be the MGF of the random variable W of interest. We study the case when W (s) = h{G (s) ; λ}, where G (s) is an MGF of G for which a random sample can be obtained, and h is a smooth function. If Ĝ (s) estimates G (s), then Ŵ (s) = h{Ĝ (s) ; λ̂} estimates W (s). Generally, it can be shown that Ŵ (s) converges to W (s) by the strong law of large numbers, which implies that F̂ (t), the cumulative distribution function (CDF) corresponding to Ŵ (s), converges to F (t), the CDF of W, almost surely. If we set Ŵ* (s) = h{Ĝ* (s) ; λ̂}, where Ĝ* (s) and λ̂* are the empirical MGF and the estimator of λ from bootstrapping, the corresponding CDF F̂* (t) can be used to construct the confidence band of F(t). In this dissertation, we show that the saddlepoint inversion of Ŵ (s) is not only fast, reliable, stable, and accurate enough for a general statistical inference, but also easy to use without deep knowledge of the probability theory regarding the stochastic process of interest. For the first part, we consider nonparametric estimation of the density and the CDF of the stationary waiting times W and Wq of an M/G/1 queue. These estimates are computed using saddlepoint inversion of Ŵ (s) determined from the Pollaczek-Khinchin formula. Our saddlepoint estimation is compared with estimators based on other approximations, including the Cramér-Lundberg approximation. For the second part, we consider the saddlepoint approximation for the busy period distribution FB (t) in a M/G/1 queue. The busy period B is the first passage time for the queueing system to pass from an initial arrival (1 in the system) to 0 in the system. If B (s) is the MGF of B, then B (s) is an implicitly defined function of G (s) and λ, the inter-arrival rate, through the well-known Kendall-Takács functional equation. As in the first part, we show that the saddlepoint approximation can be used to obtain F̂B (t), the CDF corresponding to B̂(s) and simulation results show that confidence bands of FB (t) based on bootstrapping perform well.
Open Access
The utility of near-infrared reflectance spectroscopy for wheat quality assessment
(Colorado State University. Libraries, 2010) Butler, Joshua Donald, author; Haley, Scott D., advisor; Brick, Mark A., committee member; Chapman, Phillip L., committee member; Seabourn, Bradford W., committee member
End-use quality improvement is an important objective in most wheat (Triticum aestivum L.) breeding programs. Limited sample size, destructive parameter testing, and the short duration between harvest and planting of winter wheat are challenges for testing early-generation breeding material for end-use quality parameters. Near-infrared reflectance (NIR) spectroscopy is a rapid and non-destructive technique that could facilitate early-generation selection for end-use quality. The precision and accuracy of an NIR equation for prediction purposes is dependent on the construction of a reliable calibration. The objectives of this study were to: 1) develop and validate NIR calibration models for grain volume weight, kernel characteristics, and Farinograph parameters, and 2) evaluate the performance of NIR calibration models in a breeding context for grain volume weight and single kernel characteristics. Calibration models for prediction of grain volume weight and single kernel characteristics were developed using NIR spectra and laboratory reference values from up to 10,000 samples collected from breeding nurseries under multiple environments over four crop years. Models encompassing all years of data revealed R2 (validation) of 0.73 for kernel diameter, 0.74 for kernel weight, 0.70 for kernel hardness, and 0.81 for grain volume weight. Of the Farinograph parameters, only absorption was effectively predicted using NIR calibration models for whole grain and flour with R2≥0.70. Realized heritability was estimated as a response to selection using NIR predicted values and laboratory reference values and was generally larger when using the reference values when compared to predicted values (0.17-0.77 vs. 0.05-0.77), but suggested that genetic gain was possible when using NIR models for selection. Classification errors when using the NIR models were highest in the mid-range reference values (56-66%), but could allow for divergent selection of high and low reference values. The results suggest that NIR models suitable for screening grain volume weight, SKCS kernel characteristics, and Farinograph absorption could be utilized in a breeding program and could aid in the elimination of early-generation samples with unacceptable values.
Open Access
Update of BeefCam™ tenderness prediction abilities of 14 day aged longissimus muscles
(Colorado State University. Libraries, 2010) Green, Melissa Dianne, author; Belk, Keith E., advisor; Tatum, Joseph D., committee member; Chapman, Phillip L., committee member
The research presented herein was conducted to update BeefCam™ tenderness predictive abilities of 14 day aged longissimus muscle samples by creating new regression equations. In this investigation, image data were collected from 670 carcasses at four beef packing plants using a video image analysis system, BeefCam™, and those data were used to predict the tenderness of aged (14 d), fresh beef Longissimus muscle (EM). Portions of the EM were removed from the striploin subprimal (NAMP #180) on both sides of each carcass. All EM samples remained fresh, were aged at 2°C for 14 d, and were cooked to a target internal temperature of 71°C. The EM samples collected from the right side of each carcass were assessed for tenderness by means of Warner-Bratzler shear force (WBSF) analysis, whereas samples collected from the left side of each carcass were evaluated by means of slice shear force (SSF) analysis. Data were sorted by SSF values and half the carcasses from each day of collection were utilized as a sequestered validation dataset (N = 334), while the remaining 336 carcasses constituted an instrument calibration dataset. BeefCam™ output measures were used in regression analyses to predict beef EM tenderness following aging. A regression equation was developed using the calibration dataset that correctly classified 280 carcasses out of 336 (83.3%) as tough or tender based on EM tenderness. When the same equation was applied to the sequestered validation dataset, it correctly classified 266 out of 334 (79.6%) carcasses as tough or tender. The developed regression equation was very successful in classifying tender carcasses, although BeefCam™ had difficulty properly identifying the tough carcasses. The root mean square error (RMSE), predicted residual sum of squares (PRESS) and statistics for the regression model were 0.1239, 2.418 and 0.3300, respectively. BeefCam™ repeatability has previously been verified and approved by USDA-AMS, but in this study, repeatability was determined to be 92.6% for the calibration dataset (N = 314) when a novice operated the instrument.