Among plausible causes for replicability failure, one that has not received sufficient attention is the environment in which the research is conducted. Consisting of the population, equipment, personnel, and various conditions such as location, time, and weather, the research environment can affect treatments and outcomes, and changes in the research environment that occur when an experiment is redone can affect replicability. We examine the extent to which such changes contribute to replicability failure. Our framework is that of an initial experiment that generates the data and a follow-up experiment that is done the same way except for a change in the research environment. We assume that the initial experiment satisfies the assumptions of the two-sample t-statistic and that the follow-up experiment is described by a mixed model which includes environmental parameters. We derive expressions for the effect that the research environment has on power, sample size selection, p-values, and confidence levels. We measure the size of the environmental effect with the environmental effect ratio (EER) which is the ratio of the standard deviations of environment by treatment interaction and error. By varying EER, it is possible to determine conditions that favor replicability and those that do not.

Data from multifactor HCI experiments often violates the normality assumption of parametric tests (i.e., nonconforming data). The Aligned Rank Transform (ART) is a popular nonparametric analysis technique that can find main and interaction effects in nonconforming data, but leads to incorrect results when used to conduct contrast tests. We created a new algorithm called ART-C for conducting contrasts within the ART paradigm and validated it on 72,000 data sets. Our results indicate that ART-C does not inflate Type I error rates, unlike contrasts based on ART, and that ART-C has more statistical power than a t-test, Mann-Whitney U test, Wilcoxon signed-rank test, and ART. We also extended a tool called ARTool with our ART-C algorithm for both Windows and R. Our validation had some limitations (e.g., only six distribution types, no mixed factorial designs, no random slopes), and data drawn from Cauchy distributions should not be analyzed with ART-C.

Fifty-two Holstein steers (573 ± 9.92 kg BW) were used to determine if oral administration of crystalline menthol would induce changes in endogenous secretions of IGF-1 and circulating concentrations of glucose, lactate, and plasma urea nitrogen (PUN). Steers were blocked by BW and assigned within block to treatment. Treatments consisted of 0, 0.003, 0.03, or 0.3% crystalline menthol (DM basis) added to the diet. Animals were housed in individual, partially covered pens equipped with feed bunks and automatic water fountains. On d 1 of the experiment, blood samples were obtained via jugular venipuncture at 0, 6, 12, 18, and 24 h after feeding. Treatment administration commenced on d 2, and blood samples were again drawn at 0, 6, 12, 18, and 24 h after feeding. This blood-sampling schedule was repeated on d 9, 16, 23, and 30. Plasma was analyzed for PUN, glucose, and lactate concentrations. Serum was used to analyze IGF-1 concentration. Body weights were measured on d 1, 9, 16, 23, and 30. To accompany the live animal phase, in vitro fermentations were performed using ruminal fluid cultures. Measurements included VFA concentrations and fermentative gas production for cultures containing crystalline menthol at 0, 0.003, 0.03, or 0.3% of substrate DM. Addition of menthol to the diet of steers resulted in a treatment × day interaction ( < 0.01) for concentrations of IGF-1, PUN, and plasma glucose. Cattle fed 0 and 0.003% menthol had greater serum IGF-1 concentrations on d 2 compared with steers fed 0.03% menthol. Steers fed 0% menthol had greater serum IGF-1 concentrations on d 9 compared with steers fed 0.03 and 0.3% menthol, whereas no differences were observed on d 23 or 30. Plasma glucose was similar among treatments until d 23, when steers supplemented with 0.03% menthol had lower glucose concentrations. Plasma urea nitrogen concentrations were not different among treatments; however, PUN concentrations varied by day. A linear response was detected for BW ( = 0.03), with steers consuming 0% menthol having the greatest BW and steers that consumed 0.3% menthol having the lightest BW until d 30. A menthol × day interaction was observed for daily feed deliveries ( < 0.01): cattle fed 0.3% menthol consumed less feed from d 5 through 12. Furthermore, in vitro gas production and VFA concentrations were unaffected by addition of menthol ( > 0.21). In conclusion, menthol supplementation minimally affected blood parameters associated with growth or ruminal fermentative activity.

Menthol is a naturally occurring compound classified as an essential oil that gives plants of the Mentha species their characteristic minty aroma and flavor. Menthol is used as a cooling compound in products ranging from common cold medications to pesticides and has been found to have a wide range of biological activities in different systems within the body. More recently, menthol and other essential oils have been identified as potential alternatives to feed antibiotics and growth promotants. Menthol has been observed to directly affect κ-opioid receptors. Kappa opioid receptors are located in the central nervous system, with a high density found in the hypothalamus. Menthol has been hypothesized to be capable of binding to κ-opioid receptors in the hypothalamus, stimulating neuropeptides involved in the production and release of growth hormone and leading to increased insulin-like growth factor-1 concentration, thus increasing growth. The purpose of this experiment was to evaluate changes in blood metabolites when menthol was incorporated into the diets of steers.

We analyzed methyl esters of long-chain fatty acids (LCFA) in fecal samples obtained from crossbred heifers to determine whether these compounds could be useful indicators of the presence or absence of Escherichia coli O157. Fecal samples were characterized for presence or absence of E. coli O157 using immunomagnetic separation, LCFA were determined by gas chromatography, and a stepwise regression technique was used to evaluate the relationship between presence of E. coli O157 and LCFA. Of the 39 LCFA evaluated, only eicosapentaenoic acid concentration was associated with presence of the pathogen in feces (P<0.0153). Eicosapentaenoic acid is not produced by E. coli O157; however, its increased concentration in O157-positive samples cannot be directly attributed to the pathogen. The overall lack of differences between fatty acid profiles of E. coli O157 positive and negative samples may be explained by limited sensitivity of the immunomagnetic separation technique used to classify the samples. Our results suggest that LCFA measurements had no utility for determining E. coli O157 presence in cattle feces.

Our objective was to evaluate whether feeding elevated Cu concentrations in conjunction with Linpro, a co-extruded blend of field peas and flaxseed, affected in vitro fermentation, performance, and plasma lipid profiles of fattening beef heifers. In study 1, 2 in vitro trials were conducted as randomized complete experiments with a 2×2 factorial treatment arrangement (10 or 100 mg/kg added Cu and 0 or 10% Linpro, DM basis) to determine VFA/gas production and IVDMD. Linpro contains 12% α-linolenic acid and added vitamins and minerals. In study 2, a randomized complete block experiment with a 2×2 factorial treatment arrangement was conducted with the same previously described treatment. Crossbred yearling heifers (n=261; 351±23 kg initial BW) were blocked by weight into heavy and light groups and randomly assigned to experimental pens containing 10 or 11 heifers each. In study 1, no interactions between levels of Cu and Linpro were observed. Copper concentration did not affect IVDMD (P>0.2) but increased (P<0.05) by 1.2% when Linpro was included. Final pH was not effected by added Cu (P>0.05), but pH increased when Linpro was added (P<0.05). Total VFA were greater in high-Cu treatments (P=0.038) and molar proportions were not affected (P>0.34). Linpro had no effect on total VFA (P=0.46) and molar proportions of propionate and isobutyrate increased whereas acetate and the acetate:propionate ratio decreased (P<0.01). Linpro increased the production of H2S (30% higher; P=0.05), and Cu inclusion slightly increased CO2 proportion (64.06 vs. 67.58% for Linpro vs. Cu treatments, respectively). In study 2, there were no interactions between levels of Linpro and supplemental Cu except for plasma n-6:n-3 ratio (P<0.01). Final BW were similar for cattle fed 0 and 10% Linpro (581 vs. 588 kg; P>0.20), but cattle fed diets with Linpro consumed less feed (14.08 vs. 13.59 kg/d; P<0.05) and were therefore more efficient (0.129 vs. 0.137 for 0 vs. 10% Linpro, respectively; P<0.01). Carcass traits were not affected by treatment. Feeding elevated levels of Cu did not appreciably alter PUFA proportions in plasma and LM. Plasma and LM concentrations of omega-3 fatty acids, including C18:3, C20:5, and C22:5, were greater for heifers fed Linpro (P<0.05). Increasing dietary Cu was not effective as a strategy for decreasing ruminal biohydrogenation and subsequent tissue deposition of PUFA.

Studies attempting to identify environmental risk factors for diseases can be seen to extract candidate variables from remotely sensed datasets, using a single buffer-zone surrounding locations from where disease status are recorded. A retrospective case-control study using canine leptospirosis data was conducted to verify the effects of changing buffer-zones (spatial extents) on the risk factors derived. The case-control study included 94 case dogs predominantly selected based on positive polymerase chain reaction (PCR) test for leptospires in urine, and 185 control dogs based on negative PCR. Land cover features from National Land Cover Dataset (NLCD) and Kansas Gap Analysis Program (KS GAP) around geocoded addresses of cases/controls were extracted using multiple buffers at every 500 m up to 5,000 m, and multivariable logistic models were used to estimate the risk of different land cover variables to dogs. The types and statistical significance of risk factors identified changed with an increase in spatial extent in both datasets. Leptospirosis status in dogs was significantly associated with developed high-intensity areas in models that used variables extracted from spatial extents of 500-2000 m, developed medium-intensity areas beyond 2,000 m and up to 3,000 m, and evergreen forests beyond 3,500 m and up to 5,000 m in individual models in the NLCD. Significant associations were seen in urban areas in models that used variables extracted from spatial extents of 500-2,500 m and forest/woodland areas beyond 2,500 m and up to 5,000 m in individual models in Kansas gap analysis programme datasets. The use of ad hoc spatial extents can be misleading or wrong, and the determination of an appropriate spatial extent is critical when extracting environmental variables for studies. Potential work-arounds for this problem are discussed.

Crude glycerin is the principal byproduct of biodiesel production. The raw feedstocks, animal fats and vegetable oils, yield approximately 90 lb of biodiesel and 10 lb of crude glycerin for each 100 lb of input. When ingested by cattle, glycerin has two major fates: (1) direct absorption by the rumen epithelium, and (2) fermentation by microorganisms within the rumen to generate volatile fatty acid, mainly propionate. Using glycerin in feedlot cattle diets has become common, particularly as a component of liquid feed supplements. We have evaluated the use of crude glycerin in cattle diets in previous studies and generally have observed positive effects on dry matter intake and feed efficiency when fed up to 8% of the diet on a dry matter basis. Crude glycerin can be highly variable in its composition, however, containing varying proportions of residual alcohol, soaps, and salts. Our focus in the present experiment was on the sodium content of crude glycerin. We hypothesized that the high concentration of sodium in glycerin, when combined with salt that normally is incorporated into feedlot diets, would result in abnormally high levels of sodium that could have deleterious consequences for feed consumption. The objective of this study was to evaluate feedlot performance and carcass characteristics of finishing heifers fed diets containing high levels of crude glycerin in the presence and absence of added salt.

The majority of cattle fed in commercial feedlots are processed and placed into pens without sorting into groups of uniform size and body condition. As a result of the variability in weight and condition, this management practice may lead to some cattle being fed beyond their optimal harvest point, whereas others are underconditioned and harvested prematurely, and thus fail to reach desired weight or quality grade necessary to attract available carcass premiums. Our objective was to determine if ultrasound technology could be utilized with lightweight calves as a means of predicting carcass fat thickness and yield grade outcomes. If successful, ultrasound could be a useful means of sorting cattle into uniforms groups to improve marketing.

Nursery-age pigs (n=198) were used to evaluate the difference in abscess formation at needle-free jet and conventional needle-and-syringe injection sites. Needle-free jet injection was used to administer injections in the neck and ham on one side of the animal whereas needle-and-syringe was used for neck and ham injections on the opposite side. Immediately prior to injection, the injection site surfaces were contaminated with an inoculum of Arcanobacterium pyogenes. Each pig was humanely euthanized 27 or 28 days after injections. Histopathological results showed that needle-free jet injection was associated with more abscesses than needle-and-syringe injection at both neck (P=0.0625) and ham (P=0.0313) injection sites. Out of 792 injection sites, only 13 abscesses were observed, with 12 of those present at needle-free jet injection sites. Needle-free jet injection may increase the occurrence of injection site abscesses that necessitate carcass trimming at pork processing plants.

Human diets often contain high levels of saturated fatty acids that can have deleterious health consequences such as obesity, diabetes, and heart disease. In contrast, omega-3 fatty acids, which are essential for human nutrition, are consumed at relatively low levels despite of their positive effects on health. Natural sources of omega-3 fatty acids include fresh legumes, cool-season grasses, flaxseed, and fish oil. In spite of the fact that fresh forages often are a key part of the cattle diet, beef is a relatively poor source of omega-3 fatty acids because of biohydrogenation, the action of microorganisms in the rumen that convert polyunsaturated fatty acids, including the omega-3 fats, into saturated fats. Previous research at Kansas State University has shown that feeding cattle flax-based feeds can increase concentrations of omega-3 fatty acids in beef. Researchers at Colorado State University have reported that elevated levels of dietary copper can inhibit the biohydrogenation process to yield beef with greater proportions of polyunsaturated fatty acids. Our objective was to evaluate whether feeding elevated copper concentrations in conjunction with Linpro (O&T Farms; Regina, Saskatchewan, Canada), a co-extruded blend of field peas and flaxseed, could be used to further improve the levels of omega-3 fatty acids in beef.

receiving beef heifers health of receiving beef heifers

receiving beef heifers performance of receiving beef heifers

Associations of housing, population, and agriculture census variables, and presence near public places were retrospectively evaluated as potential risk factors for canine leptospirosis using Geographic Information Systems (GIS). The sample population included 94 dogs positive for leptospirosis based on a positive polymerase chain reaction test for leptospires on urine, isolation of leptospires on urine culture, a single reciprocal serum titer of 12,800 or greater, or a four-fold rise in reciprocal serum titers over a 2–4 week period; and 185 dogs negative for leptospirosis based on a negative polymerase chain reaction test and reciprocal serum titers less than 400. Multivariable logistic regressions revealed different risk factors among different census units; however, houses lacking complete plumbing facilities [OR = 2.80, 95% C.I. = 1.82, 4.32 (census unit, block group); OR = 1.36, 95% C.I. = 1.28, 1.45 (census tract); OR = 3.02, 95% C.I. = 2.60, 3.52 (county)]; and poverty status by age (18–64) [OR = 2.04, 95% C.I. = 1.74, 2.39 (block group); OR = 1.53, 95% C.I. = 1.41, 1.67 (census tract); and OR = 1.62, 95% C.I. = 1.50, 1.76 (county)] were consistent risk factors for all census units. Living within 2500 m of a university/college and parks/forests were also significantly associated with leptospirosis status in dogs. Dogs that live under these circumstances are at higher risk for leptospirosis and pet owners should consider vaccination.

Nonparametric data from multi-factor experiments arise often in human-computer interaction (HCI). Examples may include error counts, Likert responses, and preference tallies. But because multiple factors are involved, common nonparametric tests ( e.g. , Friedman) are inadequate, as they are unable to examine interaction effects. While some statistical techniques exist to handle such data, these techniques are not widely available and are complex. To address these concerns, we present the Aligned Rank Transform (ART) for nonparametric factorial data analysis in HCI. The ART relies on a preprocessing step that "aligns" data before applying averaged ranks, after which point common ANOVA procedures can be used, making the ART accessible to anyone familiar with the F-test. Unlike most articles on the ART, which only address two factors, we generalize the ART to N factors. We also provide ARTool and ARTweb , desktop and Web-based programs for aligning and ranking data. Our re-examination of some published HCI results exhibits advantages of the ART.

Twelve ruminally cannulated crossbred Angus steers were used to evaluate ruminal fermentation characteristics and diet digestibility when 30% (DM) corn dried distillers grains with solubles (DDGS) containing 0.42 or 0.65% (DM) of dietary S was incorporated into finishing diets based on steam-flaked corn (SFC) or dry-rolled corn (DRC). The study was a replicated, balanced randomized incomplete block design with a 2 × 2 factorial arrangement of treatments. Factors consisted of dietary S concentration (0.42 and 0.65% of DM; 0.42S and 0.65S, respectively) and grain processing method (SFC or DRC). The 0.65S concentration was achieved by adding H(2)SO(4) to DDGS before mixing rations. Steers were assigned randomly to diets and individual, slatted-floor pens, and fed once daily for ad libitum intake. Two 15-d experimental periods were used, each consisting of a 12-d diet adaptation phase and a 3-d sample collection phase. Samples were collected at 2-h intervals postfeeding during the collection phase. Ruminal pH was measured immediately after sampling, and concentrations of ruminal ammonia and VFA were determined. Fecal samples were composited by steer within period and used to determine apparent total tract digestibilities of DM, OM, NDF, CP, starch, and ether extract. Feeding 0.65S tended (P = 0.08) to decrease DMI but resulted in greater apparent total tract digestibilities of DM (P = 0.04) and ether extract (P = 0.03). Ruminal pH increased (P < 0.05) in steers fed 0.65S diets, which may be attributable, in part, to decreased (P = 0.05) VFA concentrations and greater (P < 0.01) ruminal ammonia concentrations when 0.65S was fed, compared with feeding 0.42S. These effects were more exaggerated in steers fed DRC (interaction, P < 0.01), compared with steers fed SFC. Steers fed DRC-0.65S had greater (P < 0.01) acetate concentration than steers fed DRC-0.42S, but acetate concentration was not affected by S concentration when SFC was fed. Propionate concentration was decreased (P < 0.01) in steers fed SFC-0.65S compared with steers fed SFC-0.42S, but dietary S concentration had no effect on propionate concentration when DRC was fed. Butyrate concentration was less (P < 0.01) in steers fed 0.65S diets than in steers fed 0.42S. Lactate concentrations tended (P = 0.06) to decrease in steers fed 0.65S diets. Feeding DDGS with increased S concentration may decrease feed intake and ruminal VFA concentration but increase ruminal ammonia concentration.

The effects of mineral-supplement delivery system on patterns of supplement use by grazing beef cows were measured in 2 studies. Study 1 was conducted on 4 pastures grazed by pregnant, mature beef cows (BW = 562 ± 38 kg) from February to May. Study 2 was conducted on 4 pastures grazed by lactating beef cows (BW = 579 ± 54 kg) and their calves from May to September. Treatments were mineral delivered in salt-based, granular form (salty) or mineral provided in a low-protein, cooked, molasses-based block (sweet); both were fed ad libitum. The salty supplement was supplied to cattle via a covered mineral feeder; the sweet supplement was supplied via an open-topped barrel. Both salty and sweet supplements were deployed in each pasture. No additional salt was supplied to cattle. Forage use in the vicinity of each supplement-deployment site and the frequency and duration of herd visits to each supplement-deployment site were measured during four 14-d periods during study 1 and seven 14-d periods during study 2. Supplements were moved to new locations within pastures at the beginning of each period. Consumption of the sweet supplement was greater than salty during each data-collection period in study 1; however, relative differences in consumption diminished over time (treatment × time, P = 0.03). In study 2, sweet consumption was greater than salty in periods 1, 6, and 7 but was not different from salty during periods 2, 3, 4, and 5 (treatment × time, P < 0.01). Increased consumption of the sweet supplement in study 1 translated to greater frequency of herd visits to supplement-deployment sites compared with the salty sites (2.82 vs. 2.47 herd visits/d; P = 0.02) and longer herd visits to supplement-deployment sites compared with the salty sites (125.7 vs. 54.9 min/herd visit; P < 0.01). The frequency of herd visits to mineral feeding sites in study 2 was similar (P > 0.10) between treatments for periods 1 through 6; however, herds visited the sweet sites more often than salty during period 7 (P < 0.01). Herd visits to the sweet sites were longer than those to the salty sites in study 2 (83.8 vs. 51.4 min/herd visit; P < 0.01). Forage disappearance within 100 m of supplement-deployment sites was not influenced (P ≥ 0.54) by treatment in either study. Results were interpreted to suggest that the sweet supplement influenced the location of grazing cattle more strongly than the salty supplement and may be more effective for luring cattle into specific areas of pasture during the winter, spring, and early fall but not during summer.

The growing ethanol industry in the Southern Great Plains has increased the use of wet distillers grains with solubles (WDGS) in beef cattle finishing diets. Effects of corn processing method and WDGS on carbon (C) and nitrogen (N) balance were evaluated in 4 Jersey steers using respiration calorimetry chambers. A 2 × 2 factorial arrangement of treatments was used in a Latin square design. The factors consisted of corn processing method (steam flaked corn [SFC] or dry-rolled corn [DRC]) and inclusion of corn-based WDGS (0 or 30% on a DM basis). Thus, the 4 treatment combinations consisted of: (1) SFC-based diet with 0% WDGS (SFC-0); (2) SFC-based diet with 30% WDGS (SFC-30); (3) DRC-based diet with 0% WDGS (DRC-0); and (4) DRC-based diet with 30% WDGS (DRC-30). Diets were balanced for DIP and fat. Total C (including gaseous-C) excretion (P < 0.01) and methane-C (P < 0.04) were greater for cattle consuming DRC than SFC-based diets, and cattle consuming SFC diets retained a greater (P < 0.01) quantity of C than those consuming DRC diets. Inclusion of WDGS did not affect (P > 0.52) C balance, except that cattle consuming diets containing 30% WDGS excreted more (P < 0.01) C in the urine than cattle consuming diets with no WDGS. No differences in N balance were detected (P > 0.19) between grain processing methods, although apparent N digestibility was greater (P = 0.02) for cattle consuming DRCthan SFC-based diets and N retained tended (P = 0.10) to be greater for cattle consuming DRC than SFC-based diets. Due in part to greater N intake, cattle consuming diets containing 30% WDGS excreted more (P = 0.01) total N and excreted a greater (P < 0.01) quantity of N in the urine. Apparent N digestibility (g/d and % of N intake; P < 0.03) and N retained (P < 0.05) were also greater in cattle consuming 30 compared with 0% WDGS. From these results we conclude that finishing cattle excrete a greater amount of C when fed DRC compared with SFC-based diets, and that dietary inclusion of 30% WDGS increases urinary N excretion when diets are balanced for equal DIP concentration.

To validate how packaging and storage reduces Listeria monocytogenes on whole-muscle beef jerky and smoked pork and beef sausage sticks, four packaging systems (heat sealed [HS] without vacuum, heat sealed with oxygen scavenger, nitrogen flushed with oxygen scavenger [NFOS], and vacuum) and four ambient temperature storage times were evaluated. Commercially available whole-muscle beef jerky and smoked pork and beef sausage sticks were inoculated with a five-strain L. monocytogenes cocktail, packaged, and then stored at 25.5°C until enumerated for L. monocytogenes at 0, 24, 48, and 72 h and 30 days after packaging. The interaction of packaging and storage time affected L. monocytogenes reduction on jerky, but not on sausage sticks. A >2-log CFU/cm2 reduction was achieved on sausage sticks after 24 h of storage, regardless of package type, while jerky had >2-log reductions for all packaging types. At 48 h, log reductions were similar (P >0.05) for all types of jerky packaging, ranging from 1.26 to 1.72 log CFU/cm2; however, at 72 h, mean L. monocytogenes reductions were >2 log CFU/cm2, except for NFOS (1.22-log CFU/cm2 reduction). Processors could package beef jerky in HS packages with oxygen scavenger or vacuum in conjunction with a 24-h holding time as an antimicrobial process to ensure a >1-log CFU/cm2 L. monocytogenes reduction or use a 48-h holding time for HS- or NFOS-packaged beef jerky. A >3-log CFU/cm2 mean reduction was observed for all beef jerky and sausage stick packaging systems after 30 days of 25.5°C storage.