Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure

Background

Influenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are known to be responsible for a number of pandemics. A key computational issue in influenza prevention and control is the identification of molecular signatures with cross-species transmission potential. We propose an adjusted entropy-based host-specific signature identification method that uses a similarity coefficient to incorporate the amino acid substitution information and improve the identification performance. Mutations in the polymerase genes (e.g., PB2) are known to play a major role in avian influenza virus adaptation to mammalian hosts. We thus focus on the analysis of PB2 protein sequences and identify host specific PB2 amino acid signatures.

Results

Validation with a set of H5N1 PB2 sequences from 1996 to 2006 results in adjusted entropy having a 40% false negative discovery rate compared to a 60% false negative rate using unadjusted entropy. Simulations across different levels of sequence divergence show a false negative rate of no higher than 10% while unadjusted entropy ranged from 9 to 100%. In addition, under all levels of divergence adjusted entropy never had a false positive rate higher than 9%. Adjusted entropy also identifies important mutations in H1N1pdm PB2 previously identified in the literature that explain changes in divergence between 2008 and 2009 which unadjusted entropy could not identify.

Conclusions

Based on these results, adjusted entropy provides a reliable and widely applicable host signature identification approach useful for IAV monitoring and vaccine development.

Seasonal Variation in Terrestrial Invertebrate Subsidies to Tropical Streams and Implications for the Feeding Ecology of Hart’s Rivulus (Anablepsoides hartii)

Terrestrial invertebrates are important subsidies to fish diets, though their seasonal dynamics and importance to tropical stream consumers are particularly understudied. In this year-round study of terrestrial invertebrate input to two Trinidadian headwater streams with different forest canopy densities, we sought to (a) measure the mass and composition of terrestrial inputs with fall-in traps to evaluate the influences of seasonality, canopy cover, and rainfall intensity, and; (b) compare terrestrial and benthic prey importance to Anablepsoides hartii (Hart’s Rivulus), the dominant invertivorous fish in these streams, by concurrently measuring benthic and drifting invertebrate standing stocks and the volume and composition of invertebrates in Rivulus guts throughout the year. The biomass of terrestrial invertebrate fall-in was 53% higher in the wet versus dry season; in particular, ant input was 320% higher. Ant biomass fall-in also increased with the density of canopy cover among sampling locations within both streams. Greater precipitation correlated with increased ant inputs to the more open-canopied stream and increased inputs of winged insects in the more closed canopy stream. Concurrently, the biomass of benthic invertebrates was reduced by more than half in the wet season in both streams. We detected no differences in the total volume of terrestrial prey in Rivulus diets between seasons, though ants were a greater proportion of their diet in the wet season. In contrast, benthic prey were nearly absent from Rivulus diets in the wet season in both streams. We conclude that terrestrial invertebrates are a substantial year-round prey subsidy for invertivores in tropical stream ecosystems like those we studied, which may contrast to most temperate streams where such terrestrial inputs are significantly reduced in the cold season. Interestingly, the strongest seasonal pattern in these tropical streams was observed in benthic invertebrate biomass which was greatly reduced and almost absent from Rivulus diets during the wet season. This pattern is essentially the inverse of the pattern observed in many temperate streams and highlights the need for additional studies in tropical ecosystems to better understand how spatial and temporal variation in terrestrial subsidies and benthic prey populations combine to influence consumer diets and the structure of tropical stream food webs.

Using the heat generated from electrically conductive concrete slabs to reduce antibiotic resistance in beef cattle manure

Proper treatment is necessary to reduce antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in livestock manure before land application. Conventional stockpiling suffers unreliable removal efficiency, while composting can be complicated and expensive. The objective of this study was to test the feasibility of a novel heat-based technology, i.e., stockpiling manure on conductive concrete slabs, to inactivate ARB and ARGs in beef cattle manure. In this study, two independent bench-scale trials were conducted. In both trials, samples were taken from manure piles on conductive concrete slabs and regular slabs (i.e., heated and unheated piles). In the heated pile of the first trial, 25.9% and 83.5% of the pile volume met the EPA Class A and Class B biosolids standards, respectively. For the heated pile of the second trial, the two values were 43.9% and 74.2%. In both trials, nearly all forms of the total and resistant Escherichia coli and enterococci were significantly lower in the heated piles than in the unheated piles. Besides, significant reduction of ARGs in heated piles was observed in the first trial. Through this proof-of-concept study, the new technology based on conductive concrete slabs offers an alternative manure storage method to conventional stockpiling and composting with respect to reduce ARB and ARGs in manure.

Antibiotic resistance genes in swine manure slurry as affected by pit additives and facility disinfectants

Manure storage facilities are critical control points to reduce antibiotic resistance genes (ARGs) in swine manure slurry before the slurry is land applied. However, little is known about how exogenous chemicals entering the manure storage facilities may affect the fate of ARGs. The objective of this study was to analyze the impact of six commonly used pit additives and four facility disinfectants on the concentration of ARGs in swine manure slurry. Bench scale reactors, each containing approximately 50 L of liquid swine manure, were dosed with additives or disinfectants and were sampled for 40 days. Seven antibiotic resistance genes along with the intI1 gene and the 16S rRNA gene were monitored. Out of the six additives tested, Sludge Away significantly reduced the time-averaged absolute abundance of erm(C), erm(F), tet(Q), and the 16S rRNA gene as compared to the no additive control. Out of the four disinfectants tested, Tek-Trol significantly reduced the time-averaged absolute abundance of erm(B), erm(C), erm(F), intI1, tet(Q), and tet(X) than did the no-disinfectant control. According to Spearman's rank correlation, three genes erm(F), tet(Q), and tet(X) showed a strong to perfectly positive correlation and the two genes erm(B) and tet(O) showed a moderate to strong correlation in both the additive and disinfectant tests. Overall, the disinfectants were more effective in controlling the absolute abundance of ARGs than were the pit additives.

Most High-Intensity Transient Signals Are Not Associated With Specific Surgical Maneuvers

Background:

Mortality after congenital heart defect surgery has dropped dramatically in the last few decades. Current research on long-term outcomes has focused on preventing secondary neurological sequelae, for which embolic burden is suspected. In children, little is known of the correlation between specific surgical maneuvers and embolic burden. Transcranial Doppler ultrasound is highly useful for detecting emboli but has not been widely used with infants and children.

Methods:

Bilateral middle cerebral artery blood flow was continuously monitored from sternal incision to chest closure in 20 infants undergoing congenital heart defect repair or palliative surgery. Embolus counts for specific maneuvers were recorded using widely accepted criteria for identifying emboli via high-intensity transient signals (HITS).

Results:

An average of only 13% of all HITS detected during an operation were correlated with any of the surgical maneuvers of interest. The highest mean number of HITS associated with a specific maneuver occurred during cross-clamp removal. Cross-clamp placement also had elevated HITS counts that significantly differed from other maneuvers.

Conclusions:

In this study of infants undergoing cardiac surgery with cardiopulmonary bypass, the great majority of HITS detected are not definitively associated with a specific subset of surgical maneuvers. Among the measured maneuvers, removal of the aortic cross-clamp was associated with the greatest occurrence of HITS. Future recommended research efforts include identifying and confirming other sources for emboli and longitudinal outcome studies to determine if limiting embolic burden affects long-term neurological outcomes.

Corn stalk residue may add antibiotic-resistant bacteria to manure composting piles

Manure is commonly used as a fertilizer or soil conditioner; however, land application of untreated manure may introduce pathogens and antibiotic-resistant bacteria (ARB) into the soil, with harmful implications for public health. Composting is a manure management practice wherein a carbon-rich bulking agent, such as corn (Zea mays L.) stalk residue, is added to manure to achieve desirable carbon/nitrogen ratios to facilitate microbial activities and generate enough heat to inactivate pathogens, including antibiotic-resistant pathogens. However, when comparing compost piles and stockpiles for ARB reduction, we noticed that bulking agents added ARB to composting piles and compromised the performance of composting in reducing ARB. We hypothesized that ARB could be prevalent in corn stalk residues, a commonly used bulking agent for composting. To test this hypothesis, corn stalk residue samples throughout Nebraska were surveyed for the presence of ARB. Of the samples tested, 54% were positive for antibiotic-resistant Escherichia coli or enterococci using direct plating or after enrichment. Although not statistically significant, there was a trend wherein the use of pesticides tended to result in a greater prevalence of some ARB. Results from this study suggest that bulking agents can be a source of ARB in manure composting piles and highlight the importance of screening bulking agents for effective ARB reduction in livestock manure during composting.

Swine slurry characteristics as affected by selected additives and disinfectants

Current swine industry practice is to house animals in confinement facilities which capture and store feces and urine as slurry in pits below the production area. Additives and disinfectants may be introduced into the manure pits. This study was conducted to measure the effects of additives and disinfectants on temporal changes in swine slurry characteristics. Slurry from a commercial swine production facility in southeast Nebraska, USA was collected and transferred to 57 L reactors located within a greenhouse. Selected additives and disinfectants were added to the reactors and physical properties, chemical characteristics, and antibiotic concentrations were monitored for 40 days. Concentrations of dry matter (DM), total nitrogen (TN), phosphorus pentoxide (P₂O₅), calcium (Ca), magnesium (Mg), zinc (Zn), iron (Fe), manganese (Mn), and copper (Cu) were significantly greater than the Control in each of the reactors containing additives. The reactors in which the additives MOC-7, More Than Manure®, Sludge Away, and Sulfi-Doxx were introduced had significantly greater values of chemical oxygen demand (COD), total volatile solids (TVS), total suspended solids (TSS), total solids (TS), dry matter (DM), TN, P₂O₅, Ca, Mg, Zn, Fe, Mn, Cu and chlortetracycline than the other additive treatments. Concentrations of TVS and TSS were significantly lower in the reactors containing Clorox® and Virkon™ than the other disinfectant treatments. The total dissolved solids (TDS) concentration of 26,500 mg L^-1 and pH value of 7.27 obtained for the reactors containing Tek-Trol were significantly greater than measurements obtained for the other treatments. Concentrations of chlortetracycline and tiamulin of 8840 and 28.8 ng g^-1, respectively, were significantly lower for the treatments containing Tek-Trol. The sodium (Na) concentration of 1070 mg L^-1 measured in the reactors containing Clorox® was significantly greater than values for the other disinfectant treatments. The introduction of selected additives and disinfectants may influence certain physical properties, chemical characteristics, and antibiotic concentrations of swine slurry.

Influence of Setback Distance on Antibiotics and Antibiotic Resistance Genes in Runoff and Soil Following the Land Application of Swine Manure Slurry

The environmental spread of antibiotics and antibiotic resistance genes (ARGs) from the land application of livestock wastes can be a potential public health threat. The objective of this study was to assess the effects of setback distance, which determines how close manure may be applied in relation to surface water, on the transport of antibiotics and ARGs in runoff and soil following land application of swine manure slurry. Rainfall simulation tests were conducted on field plots covered with wheat residues, each of which contained an upslope manure region where slurry was applied and an adjacent downslope setback region that did not receive slurry. Results show that all three antibiotics (chlortetracycline, lincomycin, and tiamulin) and seven out of the ten genes tested (erm(B), erm(C), intI1, tet(O), tet(Q), tet(X), and the 16S rRNA gene) decreased significantly in runoff with increased setback distance. Only bla_TEM, chlortetracycline, and tiamulin decreased significantly in surface soil with increased setback distance, while the other analytes did not exhibit statistically significant trends. By using linear regression models with field data, we estimate that a setback distance between 34-67 m may allow manure-borne antibiotics and ARGs in runoff to reach background levels under the experimental conditions tested.

228 Modeling repeated measurements of diet composition

Estimating feed intake plays a key role in measuring the efficiency of feed use in livestock production systems. However, measuring feed intake in grazing environments is challenging. While the plant-wax marker methodology can be used to measure feed intake, an estimate of diet composition is also necessary. In addition, having a measure of the composition of the diet of grazing herbivores is important for grazing management and rangeland ecology. Although accurately estimating diet composition is possible using nonnegative least squares, modeling repeated measurements or relationships among individuals is not possible. Thus, the goal of this study was to develop models that account for covariance among repeated measurements and relationships among animals. These methodologies were tested on plant-wax marker fecal data from 21 beef cattle heifers, measured at two physiological stages, offered ad libitum pure red clover (Trifolium pratense) and tall fawn fescue (Festuca arundinacea) cubed hay. Plant-wax marker concentration (C27, C29, C31, C33) from the two forage species and fecal samples were measured using gas chromatography. The performance of the proposed methods was assessed by calculating normalized mean squared error (NMSE), mean absolute differences (MAD), reconstruction error (RE), mean bias, and standard error (posterior standard deviation). In addition, the intercept and slopes from regressing observed on estimated red clover proportion in the diet were tested for equality to zero and one, respectively. While modeling repeated measurements did not consistently improve the accuracy of estimation, accounting for relationship among animals appeared to improve MAD, NMSE and RE values. In addition, estimated intercept and slope from regressing observed on estimated red clover proportion did not differ from zero or one, respectively (P ≥ 0.18). While accounting for covariance among repeated measurements only marginally improved accuracy, incorporating a matrix of relationships among animals increased the reliability of estimates of their diet composition.

Dung Beetles Increase Greenhouse Gas Fluxes from Dung Pats in a North Temperate Grassland

Soil fauna plays a critical role in various ecosystem processes, but empirical data measuring its impact on greenhouse gas (GHG) emissions from rangelands are limited. We quantified the effects of dung beetles on in situ CO, CH, and NO emissions from simulated cattle dung deposits. Soil in meadows of the semiarid Nebraska Sandhills was treated with three treatments (dung pats with exposure and without exposure to dung beetles, and a no dung control). A closed-chamber method was used to measure GHG fluxes at 0, 1, 2, 3, 7, 10, 14, 21, 28, and 56 d after dung placement in the early season (June-August) and late season (July-September) in 2014 and 2015. The greatest dung beetle abundance was 6 ± 2 beetles per quarter pat on Day 7; the abundance decreased to <2 ± 0.6 on Day 14 and 28 and zero on Day 56. Dung beetles increased fluxes of CO by 0.2 g C d m, NO by 0.4 mg N d m (only in late season 2015), and CH by 0.2 mg C d m. These increases were due to beetle-made macropores that facilitated gas transport in wet dung (initial moisture = 4.6 g g on a dry-weight basis) within 7 d after dung placement. Seasonal environmental differences resulted in greater CO, NO, and CH fluxes in the early season than in the late season. This study concluded that dung beetles increased GHG fluxes from early- and late-season dung deposits on meadows of the semiarid Nebraska Sandhills.

Group screening for rare events based on incomplete block designs

Fields such as, diagnostic testing, biotherapeutics, drug development, and toxicology among others, center on the premise of searching through many specimens for a rare event. Scientists in the business of "searching for a needle in a haystack" may greatly benefit from the use of group screening design strategies. Group screening, where specimens are composited into pools with each pool being tested for the presence of the event, can be much more cost-efficient than testing each individual specimen. A number of group screening designs have been proposed in the literature. Incomplete block screening designs are described here and compared with other group screening designs. It is shown under certain conditions, that incomplete block screening designs can provide nearly a 90% cost saving compared to other group screening designs such as when prevalence is 0.001 and screening 3876 specimens with an ICB-sequential design vs. a Dorfman design. In other cases, previous group screening designs are shown to be most efficient. Overall, when prevalence is small (≤0.05) group screening designs are shown to be quite cost effective at screening a large number of specimens and in general there is no one design that is best in all situations. © 2018 American Institute of Chemical Engineers Biotechnol Progress, 35: e2770, 2019.

Response Surface Methodology for Salmonella Inactivation during Extrusion Processing of Oat Flour

An increase in the number of foodborne outbreaks and recalls due to Salmonella in low-moisture foods has resulted in the need for the development and validation of process controls to ensure their microbiological safety. Furthermore, the Food Safety Modernization Act Preventive Controls for Human Food final rule requires food processors to validate their process controls to ensure food safety. The objective of this study was to develop a response surface model to predict Salmonella inactivation in oat flour, as affected by moisture, fat content, screw speed, and temperature. Oat flour was adjusted to different moisture (14 to 26% wet basis) and fat (5 to 15% [w/w]) contents and was then inoculated with a five-strain cocktail of Salmonella. Inoculated material was extruded through a single-screw extruder running at different screw speeds (75 to 225 rpm) and temperatures (65 to 85°C), without a die. Once steady-state conditions were attained, extruded samples were collected, cooled, and stored under refrigeration, and Salmonella survivors were enumerated. A split-plot central composite second-order response surface design was used, with the central point replicated six times. Temperature showed a significant ( P < 0.0005) positive effect on microbial reduction. Moisture content showed significant linear ( P = 0.0014) and quadratic ( P = 0.0005) effects, whereas higher fat content showed a significant ( P < 0.0001) protective effect on Salmonella destruction. The screw speed did not play a major role in inactivating Salmonella, but it had a significant ( P = 0.0004) interactive effect with temperature. Results indicated that a >5.5-log reduction was achieved in oat flour extruded at a temperature above 85°C at all moisture and fat contents evaluated at a screw speed of 150 rpm. The developed response surface model can be used to identify the extrusion process conditions to achieve a desired reduction of Salmonella based on the moisture and fat contents of the product.

Evaluation of Enterococcus faecium NRRL B-2354 as a Surrogate for Salmonella During Extrusion of Low-Moisture Food

Salmonella in low-moisture foods is an emerging challenge due to numerous food product recalls and foodborne illness outbreaks. Identification of suitable surrogate is critical for process validation at industry level due to implementation of new Food Safety Modernization Act of 2011. The objective of this study was to evaluate Enterococcus faecium NRRL B-2354 as a surrogate for Salmonella during the extrusion of low-moisture food. Oat flour, a low-moisture food, was adjusted to different moisture (14% to 26% wet basis) and fat (5% to 15% w/w) contents and was inoculated with E. faecium NRRL B-2354. Inoculated material was then extruded in a lab-scale single-screw extruder running at different screw speeds (75 to 225 rpm) and different temperatures (75, 85, and 95 °C). A split-plot central composite 2nd order response surface design was used, with the central point replicated six times. The data from the selective media (m-Enterococcus agar) was used to build the response surface model for inactivation of E. faecium NRRL B-2354. Results indicated that E. faecium NRRL B-2354 always had higher heat resistance compared to Salmonella at all conditions evaluated in this study. However, the patterns of contour plots showing the effect of various product and process parameters on inactivation of E. faecium NRRL B-2354 was different from that of Salmonella. Although E. faecium NRRL B-2354 may be an acceptable surrogate for extrusion of low-moisture products due to higher resistance than Salmonella, another surrogate with similar inactivation behavior may be preferred and needs to be identified.

PRACTICAL APPLICATION

Food Safety Modernization Act requires the food industry to validate processing interventions. This study validated extrusion processing and demonstrated that E. faecium NRRL B-2354 is an acceptable surrogate for extrusion of low-moisture products. The developed response surface model allows the industry to identify process conditions to achieve a desired lethality for their products based on composition.

Genotype, environment, seeding rate, and top-dressed nitrogen effects on end-use quality of modern Nebraska winter wheat

BACKGROUND

Fine-tuning production inputs such as seeding rate, nitrogen (N), and genotype may improve end-use quality of hard red winter wheat (Triticum aestivium L.) when growing conditions are unpredictable. Studies were conducted at the Agronomy Research Farm (ARF; Lincoln, NE, USA) and the High Plains Agricultural Laboratory (HPAL; Sidney, NE, USA) in 2014 and 2015 in Nebraska, USA, to determine the effects of genotype (6), environment (4), seeding rate (3), and flag leaf top-dressed N (0 and 34 kg N ha^-1 ) on the end-use quality of winter wheat.

RESULTS

End-use quality traits were influenced by environment, genotype, seeding rate, top-dressed N, and their interactions. Mixograph parameters had a strong correlation with grain volume weight and flour yield. Doubling the recommended seeding rate and N at the flag leaf stage increased grain protein content by 8.1% in 2014 and 1.5% in 2015 at ARF and 4.2% in 2014 and 8.4% in 2015 at HPAL.

CONCLUSION

The key finding of this research is that increasing seeding rates up to double the current recommendations with N at the flag leaf stage improved most of the end-use quality traits. This will have a significant effect on the premium for protein a farmer could receive when marketing wheat. © 2017 Society of Chemical Industry.

Extraction, identification, and quantification of antioxidant phenolics from hazelnut (Corylus avellana L.) shells

Hazelnut shells are the major byproduct of the hazelnut industry. The objectives of this study were to optimize the conditions for extracting phenolics and to identify and quantify the phenolics in hazelnut shells. Preliminary optimization showed that a high recovery of phenolics could be achieved with shell particle size less than 0.5mm when extracted with acetone at 50°C. Response surface experiments showed that a 10g/l liquid to solid ratio, 58% acetone, and 12h extraction time yielded the highest amount of phenolics. Twenty-seven phenolic compounds were identified in hazelnut shells by mass spectrometry. Coumaroylquinic acid, epicatechin gallate, quercetin, and six other phenolics were identified in hazelnut shells for the first time. The most abundant phenolics in hazelnut shells were catechin, epicatechin gallate, and gallic acid, as quantified by high performance liquid chromatography (HPLC). These results can be useful for the development of industrial extraction processes of natural antioxidants from hazelnut shells.

Type 2 BVDV Npro suppresses IFN-1 pathway signaling in bovine cells and augments BRSV replication

Bovine viral diarrhea virus (BVDV) infection induces immunosuppression and in conjunction with bovine respiratory syncytial virus (BRSV) contributes to the bovine respiratory disease complex. Bovine turbinate cells were single or co-infected with type 2 BVDV wild-type (BVDV2-wt), its dysfunctional N^pro mutant (BVDV2-E), and/or BRSV. BVDV2-E significantly up-regulated PKR, IRF-7, TBK-1, IRF-3, and IFN-β mRNAs based on real-time Q-RT-PCR. BRSV-infected cells expressed significantly up-regulated PKR, IRF-3, IRF-7, and IFN-β mRNAs, whereas BVDV2-wt, but not BVDV2-E, abolished this up-regulation in co-infection. No significant differences were observed in MAVS, NF-κB, and PIN-1 mRNAs. A dual-luciferase reporter assay showed that BVDV2-wt significantly increased NF-κB activity compared to BVDV2-E, while BVDV2-E significantly increased IFN-β activity compared to BVDV2-wt. The BRSV titer and RNA levels significantly increased in cells co-infected with BRSV/BVDV2-wt compared to cells co-infected with BRSV/BVDV2-E or infected with BRSV alone. This data supports the synergistic action of BVDV2-wt and BRSV inhibition of IFN-1.

Experimental acute infection of alpacas with Bovine viral diarrhea virus 1 subgenotype b alters peripheral blood and GALT leukocyte subsets

Bovine viral diarrhea virus (BVDV) is a pathogen in cattle and alpacas ( Vicugna pacos), causing acute and persistent BVDV infections. We characterized the effect of acute BVDV infection on the immune system of alpacas by determining lymphocyte subpopulations in peripheral blood and gut-associated lymphoid tissues (GALT) as well as serum interferon levels. Alpacas were experimentally infected with BVDV-1b (strain CO-06). Peripheral blood leukocytes were isolated at 0, 3, 6, and 9 d postinfection (dpi), and leukocytes of GALT at 9 dpi, and evaluated using flow cytometry. Serum interferon levels were determined daily. Flow cytometric analyses of peripheral blood leukocytes showed a significant decrease in CD4+, CD8+, and αβ T-lymphocytes at 3 dpi. CD8+ lymphocytes were significantly increased, and activated lymphocytes were significantly decreased in the C3-stomach region in BVDV-infected alpacas. Serum interferon concentrations significantly increased in BVDV-infected alpacas at 3-6 dpi, peaking at 3 dpi. Our study confirms that BVDV can be a primary acute pathogen in alpacas and that it induces an interferon response and alters leukocyte subset populations. The changes in the proportion of T-lymphocytes during the early stages of BVDV infection may result in transient immunosuppression that may contribute to secondary bacterial and viral infections, similar to cattle.

Effects of soil texture and drought stress on the uptake of antibiotics and the internalization of Salmonella in lettuce following wastewater irrigation

Treated wastewater is expected to be increasingly used as an alternative source of irrigation water in areas facing fresh water scarcity. Understanding the behaviors of contaminants from wastewater in soil and plants following irrigation is critical to assess and manage the risks associated with wastewater irrigation. The objective of this study was to evaluate the effects of soil texture and drought stress on the uptake of antibiotics and the internalization of human pathogens into lettuce through root uptake following wastewater irrigation. Lettuce grown in three soils with variability in soil texture (loam, sandy loam, and sand) and under different levels of water stress (no drought control, mild drought, and severe drought) were irrigated with synthetic wastewater containing three antibiotics (sulfamethoxazole, lincomycin and oxytetracycline) and one Salmonella strain a single time prior to harvest. Antibiotic uptake in lettuce was compound-specific and generally low. Only sulfamethoxazole was detected in lettuce with increasing uptake corresponding to increasing sand content in soil. Increased drought stress resulted in increased uptake of lincomycin and decreased uptake of oxytetracycline and sulfamethoxazole. The internalization of Salmonella was highly dependent on the concentration of the pathogen in irrigation water. Irrigation water containing 5 Log CFU/mL Salmonella resulted in limited incidence of internalization. When irrigation water contained 8 Log CFU/mL Salmonella, the internalization frequency was significantly higher in lettuce grown in sand than in loam (p = 0.009), and was significantly higher in lettuce exposed to severe drought than in unstressed lettuce (p = 0.049). This work demonstrated how environmental factors affected the risk of contaminant uptake by food crops following wastewater irrigation.

Effect of waxy (Low Amylose) on Fungal Infection of Sorghum Grain

Loss of function mutations in waxy, encoding granule bound starch synthase (GBSS) that synthesizes amylose, results in starch granules containing mostly amylopectin. Low amylose grain with altered starch properties has increased usability for feed, food, and grain-based ethanol. In sorghum, two classes of waxy (wx) alleles had been characterized for absence or presence of GBSS: wx(a) (GBSS(-)) and wx(b) (GBSS(+), with reduced activity). Field-grown grain of wild-type; waxy, GBSS(-); and waxy, GBSS(+) plant introduction accessions were screened for fungal infection. Overall, results showed that waxy grains were not more susceptible than wild-type. GBSS(-) and wild-type grain had similar infection levels. However, height was a factor with waxy, GBSS(+) lines: short accessions (wx(b) allele) were more susceptible than tall accessions (undescribed allele). In greenhouse experiments, grain from accessions and near-isogenic wx(a), wx(b), and wild-type lines were inoculated with Alternaria sp., Fusarium thapsinum, and Curvularia sorghina to analyze germination and seedling fitness. As a group, waxy lines were not more susceptible to these pathogens than wild-type, supporting field evaluations. After C. sorghina and F. thapsinum inoculations most waxy and wild-type lines had reduced emergence, survival, and seedling weights. These results are valuable for developing waxy hybrids with resistance to grain-infecting fungi.

Utilizing a Preplant Soil Test for Predicting and Estimating Root Rot Severity in Sugar Beet in the Central High Plains of the United States

Aphanomyces cochlioides and Rhizoctonia solani are important soilborne pathogens causing root diseases that are primary constraints to sugar beet production in Nebraska, Colorado, and Wyoming. These types of diseases are difficult to control because they are often not noticed until substantial damage has already occurred. Efforts to manage them would be more effective if techniques were available that were more predictive than reactive. Therefore, a preplant soil test was developed to estimate the relative pathogen populations in the soil and to predict potential root disease problems later in the growing season. Preplant soil samples collected from fields to be sown with sugar beet were planted with a susceptible cultivar and tests were conducted for 1 month in the greenhouse. A preplant disease index was developed based on the time period during the test that seedlings became infected and was calculated on a 0-to-100 scale. Disease index values were compared with yields obtained from the same fields after harvest. Analysis of data collected for 5 years (2003 to 2007) with analysis of covariance revealed a strong relationship between the preplant disease index values and recoverable sucrose and root yields but not sucrose concentration. Results indicated that, for each unit increase in the preplant disease index, root yield decreased by 0.27 metric tons (270 kg) per hectare (P < 0.05, R² = 0.44) and recoverable sucrose decreased by 49 kg/ha (P < 0.05, R² = 0.45). We concluded that this preplant soil test can accurately predict root disease potential due to R. solani and A. cochlioides, and has the potential to help producers make effective management decisions in production fields using the index procedure. This soil assay has additionally provided new information on the biology, incidence, and distribution of root pathogens in production fields throughout the Central High Plains.

Race/ethnicity and income in relation to the home food environment in US youth aged 6 to 19 years

BACKGROUND

The home food environment is complex and has the potential to influence dietary habit development in young people. Several factors may influence the home food environment, including income and race/ethnicity.

OBJECTIVE

To examine the relationship of income and race/ethnicity with three home food environment factors (ie, food availability frequency, family meal patterns [frequency of family and home cooked meals], and family food expenditures).

DESIGN

A cross-sectional analysis of the National Health and Nutrition Examination Survey (NHANES).

PARTICIPANTS

A total of 5,096 youth aged 6 to 19 years from a nationally representative sample of US individuals participating in NHANES 2007-10.

STATISTICAL ANALYSES PERFORMED

Prevalence of food availability frequency was assessed for the entire sample, race/ethnicity, poverty income ratio (PIR), and race/ethnicity stratified by PIR. Mean values of family meal patterns and food expenditures were calculated based on race/ethnicity, PIR, and race/ethnicity stratified by PIR using analysis of variance and least squares means. Tests of main effects were used to assess differences in food availability prevalence and mean values of family meal patterns and food expenditures.

RESULTS

Non-Hispanic whites had the highest prevalence of salty snacks (51.1%±1.5%) and fat-free/low-fat milk (39.2%±1.7%) always available. High-income homes had the highest prevalence of fruits (75.4%±2.4%) and fat-free/low-fat milk (38.4%±2.1%) always available. Differences were found for prevalence of food availability when race/ethnicity was stratified by PIR. Non-Hispanic blacks had the lowest prevalence of fat-free/low-fat milk always available across PIR groups. Differences in mean levels of family meal patterns and food expenditures were found for race/ethnicity, PIR, and race/ethnicity stratified by PIR.

CONCLUSIONS

Race/ethnicity and PIR appear to influence food availability, family meal patterns, and family food expenditures in homes of youth. Knowledge of factors that influence the home food environment could assist in developing effective strategies to improve food environments for young people.

Use of Enterococcus faecium as a surrogate for Salmonella enterica during extrusion of a balanced carbohydrate-protein meal

Multiple outbreaks of salmonellosis have been associated with the consumption of low-moisture products, including extruded products. Therefore, there is a need for a nonpathogenic, surrogate microorganism that can be used to validate extrusion processes for Salmonella. The objective of this research was to determine if Enterococcus faecium NRRL B-2354 is an adequate surrogate organism for Salmonella during extrusion. Extrusions at different temperatures were done in material contaminated with both organisms. Results indicated that the minimum temperature needed to achieve a 5-log reduction of E. faecium was 73.7°C. Above 80.3°C, the enumeration of E. faecium showed counts below the detectable levels (<10 CFU g(- 1)). Salmonella was reduced by 5 log at 60.6°C, and above 68.0°C the levels of this organism in the product were below the detection limit of the method. The data show that E. faecium is inactivated at higher temperatures than Salmonella, indicating that its use as a surrogate would provide an appropriate margin of error in extrusion processes designed to eliminate this pathogen. Attempting to minimize risk, the industry could validate different formulations, in combination with thermal treatments, using E. faecium as a safer alternative for those validation studies.

Distribution of lymphoid depletion and viral antigen in alpacas experimentally infected with Bovine viral diarrhea virus 1

It was hypothesized that acute postnatal Bovine viral diarrhea virus 1 (BVDV-1) infection leads to leukopenia and lymphoid depletion of gut-associated lymphoid tissues similar to acute disease in calves. The objectives of the current study were to characterize the pathologic effects, viremia, viral shedding, and viral antigen deposition in 6–24-month-old, acutely infected alpacas following experimental infection with noncytopathic BVDV-1 subgenotype 1b (BVDV C0-6). The BVDV-1 isolate was obtained from a cria with naturally occurring persistent infection. Lymphocytopenia occurred 3–7 days postinfection, with a 50% reduction in peripheral lymphocytes in infected alpacas. Depletion of B-cell populations in gut-associated lymphoid tissues was evident microscopically. Populations of T cells in parafollicular zones and in nodular aggregates along the superficial submucosa remained intact. The BVDV antigen was deposited most consistently in submucosal gastrointestinal aggregated lymphoid tissues of ileum, proximal colon, and stomach compartment three. Viral antigen was more variably evident in other lymphoid tissues. Antigen distribution correlated well with histologic lesions in gastrointestinal aggregated lymphoid tissues, confirming the role of virus in lymphoid depletion. Nasal shedding was detected in all challenged alpacas on day 6 and in 4 out of 12 challenged alpacas on day 9. Viremia was present as early as day 3, and present in all challenged alpacas on days 5, 6, 7, and 9 postchallenge. Lymphocytopenia and depletion of gastrointestinal aggregated lymphoid tissues associated with acute BVDV-1 infection likely results in immune compromise and is expected to exacerbate concurrent infections even though uncomplicated BVDV-1 infection was clinically unapparent.

Analysis of the fate and transport of nC₆₀ nanoparticles in the subsurface using response surface methodology

Predicting the distribution of engineered nanomaterials (ENMs) in the environment will provide critical information for risk assessment and policy development to regulate these emerging contaminants. The fate and transport of ENMs in natural subsurface environments are complicated by various factors, such as hydraulic gradient, initial release concentration, nanoparticle size, and collision efficiency factor. Based on advanced statistical methodologies (i.e., response surface methodology (RSM)), we explore simple relationships between key factors that control ENM transport (collision efficiency factor, particle size, hydraulic gradient, and initial release concentration) and key parameters that describe the ENM concentration distribution in porous media (maximum standardized concentration, the mass percentage of injected nanoparticle attached in the aquifer, the x-centroid of aqueous phase nC₆₀ plume, and the x-centroid of attached phase nC₆₀ distribution). Hypothetical scenarios for the release of nanoparticles into an aquifer were simulated numerically with randomly generated permeability fields that were based on mildly and highly heterogeneous sites. RSM was used to develop polynomial regression equations based on a statistical experimental design. High R-squared values (greater than 0.9) of the regression equations were obtained for all the models developed based on the mildly heterogeneous site. On the highly heterogeneous site, the R-squared value of the regression equation for the percentage of nanoparticles attached (by mass) was more than 0.9. The ability to accurately estimate aqueous phase ENM concentration distribution using simple regression equations is particularly critical for risk assessment. Even though the correlations developed in this study were site and scenario specific, this work represents a first effort of applying RSM for predicting the distribution of engineered nanomaterials in porous media.

Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus

Background

The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).

Results

A total of 1,007 PAS domains and 686 PDC domains distributed over 1,174 proteins were identified. For 28 Gram-positive bacteria, the distribution, organization, and molecular evolution of PDC/PAS domains were analyzed in greater detail, with a special emphasis on the genus Staphylococcus. Compared to other bacteria the staphylococci have relatively fewer proteins (6–9) containing PDC/PAS domains. As a general rule, the staphylococcal genomes examined in this study contain a core group of seven PDC/PAS domain-containing proteins consisting of WalK, SrrB, PhoR, ArlS, HssS, NreB, and GdpP. The exceptions to this rule are: 1) S. saprophyticus lacks the core NreB protein; 2) S. carnosus has two additional PAS domain containing proteins; 3) S. epidermidis, S. aureus, and S. pseudintermedius have an additional protein with two PDC domains that is predicted to code for a sensor histidine kinase; 4) S. lugdunensis has an additional PDC containing protein predicted to be a sensor histidine kinase.

Conclusions

This comprehensive analysis demonstrates that variation in PDC/PAS domains among bacteria has limited correlations to the genome size or pathogenicity; however, our analysis established that bacteria having a motile phase in their life cycle have significantly more PDC/PAS-containing proteins. In addition, our analysis revealed a tremendous amount of variation in the number of PDC/PAS-containing proteins within genera. This variation extended to the Staphylococcus genus, which had between 6 and 9 PDC/PAS proteins and some of these appear to be previously undescribed signaling proteins. This latter point is important because most staphylococcal proteins that contain PDC/PAS domains regulate virulence factor synthesis or antibiotic resistance.

Atrazine and nitrate in public drinking water supplies and non-hodgkin lymphoma in nebraska, USA

A secondary analysis of 1999-2002 Nebraska case-control data was conducted to assess the risk of non-Hodgkin lymphoma (NHL) associated with exposure to nitrate- and atrazine-contaminated drinking water. Water chemistry data were collected and weighted by well contribution and proximity of residence to water supply, followed by logistic regression to determine odds ratios (OR) and 95% confidence intervals (CI). We found no association between NHL risk and exposure to drinking water containing atrazine or nitrate alone. Risk associated with the interaction of nitrate and atrazine in drinking water was elevated (OR, 2.5; CI, 1.0-6.2). Risk of indolent B-cell lymphoma was higher than risk of aggressive B-cell lymphoma (indolent: OR, 3.5; CI, 1.0-11.6 vs. aggressive: OR, 1.9; CI, 0.6-5.58). This increased risk may be due to in vivo formation and subsequent metabolism of N-nitrosoatrazine. A larger study is warranted to confirm our findings.

Distinguishing between yield advances and yield plateaus in historical crop production trends

Food security and land required for food production largely depend on rate of yield gain of major cereal crops. Previous projections of food security are often more optimistic than what historical yield trends would support. Many econometric projections of future food production assume compound rates of yield gain, which are not consistent with historical yield trends. Here we provide a framework to characterize past yield trends and show that linear trajectories adequately describe past yield trends, which means the relative rate of gain decreases over time. Furthermore, there is evidence of yield plateaus or abrupt decreases in rate of yield gain, including rice in eastern Asia and wheat in northwest Europe, which account for 31% of total global rice, wheat and maize production. Estimating future food production capacity would benefit from an analysis of past crop yield trends based on a robust statistical analysis framework that evaluates historical yield trajectories and plateaus.

Optimal design of mixed-effects PK/PD models based on differential equations

There is a vast literature on the analysis of optimal design of nonlinear mixed-effects models (NLMMs) described by ordinary differential equations (ODEs) with analytic solution. However, much less has been published on the design of trials to fit such models with nonanalytic solution. In this article, we use the "direct" method to find parameter sensitivities, which are required during the optimization of models defined as ODEs, and apply them to find D-optimal designs for various specific situations relevant to population pharmacokinetic studies using a particular model with first-order absorption and elimination. In addition, we perform two simulation studies. The first one aims to show that the criterion computed from the development of the Fisher information matrix expression is a good measure to compare and optimize population designs, thus avoiding a large number of simulations; In the second one, a sensitivity analysis with respect to parameter misspecification allows us to compare the robustness of different population designs constructed in this article.

Variation in Sclerotinia sclerotiorum Bean Isolates from Multisite Resistance Screening Locations

There is no complete resistance to Sclerotinia sclerotiorum, cause of white mold in dry bean (Phaseolus vulgaris). Variable resistance expression is one problem in screening for improved white mold resistance. With no previous information in the literature, pathogen variation in multisite screening nurseries was evaluated as one cause of diverse resistance expression. In all, 10 isolates of S. sclerotiorum used in greenhouse screening and 146 isolates collected from nine white mold field screening nurseries in major bean production areas in the United States were compared using mycelial compatibility groupings (MCGs) and an aggressiveness test. These 10 greenhouse screening isolates formed six MCGs. Among 156 field and greenhouse isolates, 64 MCGs were identified and 36 of those were each composed of a single unique isolate. Significant differences in isolate aggressiveness were found between some isolates in different MCGs but the isolates within an MCG did not differ in aggressiveness. High isolate variation found within and between field locations could influence the disease phenotype of putative white mold resistant germplasm. We next compared genotype and phenotype of isolates from screening nurseries and those from producer fields. Variability found in and among screening locations did reflect variability found in the four producer fields sampled. White mold resistance screening can be improved by knowledge of isolate genotypic and phenotypic characteristics.

Effects of Integrating Cultivar Resistance and Fungicide Application on Fusarium Head Blight and Deoxynivalenol in Winter Wheat

Fusarium head blight (FHB) or scab, incited by Fusarium graminearum, can cause significant economic losses in small grain production. Five field experiments were conducted from 2007 to 2009 to determine the effects on FHB and the associated mycotoxin deoxynivalenol (DON) of integrating winter wheat cultivar resistance and fungicide application. Other variables measured were yield and the percentage of Fusarium-damaged kernels (FDK). The fungicides prothioconazole + tebuconazole (formulated as Prosaro 421 SC) were applied at the rate of 0.475 liters/ha, or not applied, to three cultivars (experiments 1 to 3) or six cultivars (experiments 4 and 5) differing in their levels of resistance to FHB and DON accumulation. The effect of cultivar on FHB index was highly significant (P < 0.0001) in all five experiments. Under the highest FHB intensity and no fungicide application, the moderately resistant cultivars Harry, Heyne, Roane, and Truman had less severe FHB than the susceptible cultivars 2137, Jagalene, Overley, and Tomahawk (indices of 30 to 46% and 78 to 99%, respectively). Percent fungicide efficacy in reducing index and DON was greater in moderately resistant than in susceptible cultivars. Yield was negatively correlated with index, with FDK, and with DON, whereas index was positively correlated with FDK and with DON, and FDK and DON were positively correlated. Correlation between index and DON, index and FDK, and FDK and DON was stronger in susceptible than in moderately resistant cultivars, whereas the negative correlation between yield and FDK and yield and DON was stronger in moderately resistant than in susceptible cultivars. Overall, the strongest correlation was between index and DON (0.74 ≤ R ≤ 0.88, P ≤ 0.05). The results from this study indicate that fungicide efficacy in reducing FHB and DON was greater in moderately resistant cultivars than in susceptible ones. This shows that integrating cultivar resistance with fungicide application can be an effective strategy for management of FHB and DON in winter wheat.

Correlation of omega-3 fatty acids intakes with acculturation and socioeconomic status in midwestern Latinas

BACKGROUND

Low socioeconomic status (SES) and acculturation of Latino immigrants in the U.S. are linked to a decrease in diet quality.

METHODS

Interviews were conducted with 162 first generation Latinas to examine the association of SES and acculturation with intake of omega-3 (n - 3) fatty acids. Each participant provided dietary intake by use of a validated n - 3 food frequency questionnaire administered twice, 4 weeks apart, three 24-h recalls, sociodemographic information and completed the 5-item Short Acculturation Scale.

RESULTS

Mean intakes of Total n - 3, α-linolenic acid (ALA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) (g/d) were 1.2 ± 0.7, 1.1 ± 0.6, and 0.1 ± 0.1, respectively. After adjusting for energy intake, education was significantly correlated with EPA + DHA intakes, and acculturation was significantly correlated with Total n - 3, ALA and EPA + DHA intakes. Foods sources of EPA + DHA eaten by at least 50% of participants were chicken, shrimp, tuna and eggs.

DISCUSSION

Given the beneficial cardiovascular effects of n - 3 fatty acids, it is important to understand sociocultural factors affecting adequate intake towards an improvement in diet quality in minorities.

Structural equation modeling of gene-environment interactions in coronary heart disease

Coronary heart disease (CHD) is a complex disease, which is influenced not only by genetic and environmental factors but also by gene-environment (GE) interactions in interconnected biological pathways or networks. The classical methods are inadequate for identifying GE interactions due to the complex relationships among risk factors, mediating risk factors (e.g., hypertension, blood lipids, and glucose), and CHD. Our aim was to develop a two-level structural equation model (SEM) to identify genes and GE interactions in the progress of CHD to take into account the causal structure among mediating risk factors and CHD (Level 1), and hierarchical family structure (Level 2). The method was applied to the Framingham Heart Study (FHS) Offspring Cohort data. Our approach has several advantages over classical methods: (1) it provides important insight into how genes and contributing factors affect CHD by investigating the direct, indirect, and total effects; and (2) it aids the development of biological models that more realistically reflect the complex biological pathways or networks. Using our method, we are able to detect GE interaction of SERPINE1 and body mass index (BMI) on CHD, which has not been reported. We conclude that SEM modeling of GE interaction can be applied in the analysis of complex epidemiological data sets.

Effect of the viral protein Npro on virulence of bovine viral diarrhea virus and induction of interferon type I in calves

Objective—To characterize the influence of the viral protein Npro on virulence of bovine viral diarrhea virus (BVDV) and on type I interferon responses in calves.

Animals—10 calves, 4 to 6 months of age.

Procedures—BVDV virulence and type I interferon responses of calves (n = 5) infected with a noncytopathic BVDV with a deleted Npro were compared with those of calves (5) infected with a noncytopathic BVDV with a functional Npro. Rectal temperatures, clinical signs, platelet counts, and total and differential WBC counts were evaluted daily. Histologic examinations and immunohistochemical analyses of tissues were conducted to assess lesions and distribution of viral antigens, respectively. Serum type I interferon concentrations were determined.

Results—Calves infected with Npro-deleted BVDV developed leukopenia and lymphopenia, without developing increased rectal temperatures or lymphoid depletion of target lymphoid organs. There was minimal antigen deposition in lymphoid organs. Calves infected with Npro BVDV developed increased rectal temperatures, leukopenia, lymphopenia, and lymphoid depletion with marked BVDV antigen deposition in lymphatic tissues. Interferon type I responses were detected in both groups of calves.

Conclusions and Clinical Relevance—Deletion of Npro resulted in attenuation of BVDV as evidenced by reduced virulence in calves, compared with BVDV with a functional Npro. Deletion of Npro did not affect induction of type I interferon. The Npro-deleted BVDV mutant may represent a safe noncytopathic virus candidate for vaccine development.

Virulence Diversity of the Common Bean Rust Pathogen Within and Among Individual Bean Fields and Development of Sampling Strategies

There is a dearth of information on pathogen variation within an individual field. In this study, virulence diversity of Uromyces appendiculatus, cause of bean rust, within individual fields was investigated. From six bean fields in the United States, Honduras, Dominican Republic, and South Africa, 380 U. appendiculatus isolates were differentiated into 65 virulence phenotypes on bean lines containing Andean- and Middle American-derived rust resistance genes. Race variation among bean rust isolates from different geographic regions was found, and virulence phenotypes found in fields from tropical and subtropical regions were more virulent and diverse than those found in fields from temperate regions. The variance components between fields was greater than the variance within a field based on mean disease score on 12 differentials but the variance components within a field were greater than the variances between fields based on number of virulence phenotypes. This is the first report that multiple site samples are needed to represent the fungal virulence diversity in a diseased field. In developing sampling plans, the entire cost of sampling one field is higher than the cost of taking more samples; therefore, to estimate virulence diversity variation, we recommend selecting fewer fields and collecting more samples per field.

Chemical and sensory properties of beef of known source and finished on wet distillers grains diets containing varying types and levels of roughage

Beef knuckles (n = 160) were obtained from source-verified cattle finished on 30% wet distillers grains plus solubles enriched with varying levels of alfalfa hay (4 or 8%), corn silage (6 or 12%), or corn stalks (3 or 6%) based on NDF. Proximate analysis, pH, oxidation-reduction potential, fatty acid composition, and sensory analysis were conducted on the rectus femoris muscle to determine if roughage inclusion, in conjunction with wet distillers grains plus solubles and cattle source, affects beef flavor with particular interest in liver-like off-flavor. Proximate analysis, fat content, and oxidation-reduction potential were unaffected (P ge;0.129) by diet or source. For s.c. adipose tissue, cattle from Nebraska (NE) had greater amounts of MUFA (P = 0.048) and unsaturated fatty acids (P = 0.068) but less SFA (P = 0.065) when compared with cattle from South Dakota. Diet affected s.c. adipose tissue levels of 15:0, 17:0, and n-3 fatty acids in which cattle from NE finished on the low corn stalk diet had (P < or =0.050) lower levels. Cattle from NE had (P < or = 0.049) greater i.m. adipose proportions of 13:0 and CLA. Dietary effects (P < or = 0.050) were observed for i.m. adipose tissue proportions of 16:0, 18:1(n-9), 18:2(n-6), 20:4(n-6), 22:5(n-3), MUFA, PUFA, and n-6 fatty acids. Sensory analysis revealed that cattle from NE were (P < or = 0.023) less juicy and had less bloody notes when compared with cattle from South Dakota. Cattle finished on the low alfalfa diet were (P < or = 0.014) more tender and juicy but had more bloody notes. No (P ge; 0.670) dietary or source effects were noted for liver-like off-flavor. Subcutaneous amounts of 18:2(n-6 trans) (r = -0.17) were inversely related to the incidence of liver-like off-flavor, whereas 20:1(n-9) (r = 0.21), CLA cis-9, trans-11 (r = 0.16) were directly related. Data from this study indicate that type and level of roughage inclusion and cattle source have minimal effects on fatty acid profiles and sensory properties of the musculus rectus femoris. However, individual fatty acids of s.c. and i.m. adipose tissue were significantly correlated with liver-like off-flavor.

Unsaturated fatty acids and sodium affect the liver-like off-flavor in cooked beef

Beef knuckles (n = 60) were chosen from a population of 328 knuckles to test a selection procedure and determine the potential causes of liver-like off-flavor. In phase I, 2 independent panelists were allowed to smell the aromas or smell and taste samples of cooked beef to determine the presence or absence of the liver-like off-flavor and off-flavor intensity. The panelists tested knuckles from 5 feedlots, but only identified 29 as having an off-flavor. A kappa statistic was generated to assess the level of agreement of the 2 panelists that indicated the panelists moderately or substantially agreed when judgments were based on smell exclusively or smelling and tasting, respectively. Although the agreement was acceptable (kappa = 0.57 and 0.76), there was not enough variation in the liver-like off-flavor and off-flavor intensity for the 2 panelists to detect differences compared with an independent sensory panel. Phase II identified factors that led to the development of the liver-like off-flavor in beef. The M. rectus femoris from knuckles identified from phase I were used. Sensory analysis, proximate composition, heme iron, mineral content, and fatty acid analyses were conducted. Stepwise regression was used to identify factors contributing to the liver-like off-flavor. Specifically, Na, 16:1, cis 18:1(n-7), 20:2(n-6), and 20:3(n-6) fatty acids explained (P = 0.021) 46% of the variation of the liver-like off-flavor. Although previously reported as playing a role in the development of the liver-like off-flavor, iron, heme iron, and pH had no effect in this study.

Characterization of protection against systemic infection and disease from experimental bovine viral diarrhea virus type 2 infection by use of a modified-live noncytopathic type 1 vaccine in calves

Objective—To evaluate protection resulting from use of a modified-live noncytopathic bovine viral diarrhea virus (BVDV) type 1 vaccine against systemic infection and clinical disease in calves challenged with type 2 BVDV.

Animals—10 calves, 5 to 7 months of age.

Procedures—Calves were allocated (n = 5/group) to be nonvaccinated or vaccinated SC on day 0 with BVDV 1 (WRL strain). Calves in both groups were challenged intranasally with BVDV type 2 isolate 890 on day 21. Rectal temperatures and clinical signs of disease were recorded daily, and total and differential WBC and platelet counts were performed. Histologic examinations and immunohistochemical analyses to detect lesions and distribution of viral antigens, respectively, were performed.

Results—After challenge exposure to BVDV type 2, nonvaccinated calves developed high rectal temperatures, increased respiratory rates, viremia, leukopenia, lymphopenia, and infection of the thymus. Vaccinated calves did not develop high rectal temperatures or clinical signs of respiratory tract disease. Vaccinated calves appeared to be protected against systemic replication of virus in that they did not develop leukopenia, lymphopenia, viremia, or infection of target organs, and infectious virus was not detected in peripheral blood mononuclear cells or the thymus.

Conclusions and Clinical Relevance—The modified-live BVDV type 1 vaccine protected against systemic infection and disease after experimental challenge exposure with BVDV type 2. The vaccine protected calves against infection and viremia and prevented infection of target lymphoid cells.

Statistical adjustment for misclassification of seat belt and alcohol use in the analysis of motor vehicle accident data

The use of seat belts and alcohol is often mis-reported in police motor vehicle accident reports for a number of reasons. To avoid penalties, occupants often over report seat belt use and under report alcohol use. Police officers sometimes fail to account for evidence such as presence of belt burn, condition of belts, odor of alcohol, crash patterns, etc. Biased conclusions result when using misclassified accident data to estimate the effectiveness of seat belts in preventing injuries and reducing medical costs. We investigated the effects of misclassification of seat belt and alcohol use on the odds ratio of injury as well as medical costs. A statistical method and a SAS program were developed to adjust odds ratios of injury and medical cost estimates to account for misclassification of seat belts and alcohol use. The method allowed for incorporation of variables that could affect misclassification of seat belt and alcohol use. We conducted a Monte Carlo simulation and found that when there were large differences between the misclassification rates for major and minor injury, the unadjusted odds ratio could have up to a 90% bias while our adjusted odds ratio was effectively unbiased. To illustrate the method, we estimated the misclassification rates of seat belt and alcohol use by comparing merged police and hospital reports from Nebraska motor vehicle accident data sets (1996-1997) and then evaluated the bias of the odds ratio of injury and medical costs estimates due to misclassification. Our results showed that the bias of the odds ratio of injury and medical costs due to misclassification of seat belts and alcohol use depended both on the amount of misclassification and the reported frequencies. Misclassification about seat belt and alcohol use only slightly biased the unadjusted odds ratio estimates and mean hospital charge, while misclassification resulted in approximately a 69% underestimate of the total medical costs savings due to seatbelts. However, due to the small size of the merged Nebraska police and hospital data set used to estimate misclassification rates, these results are likely somewhat imprecise.

Consumer sensory acceptance and value of domestic, Canadian, and Australian grass-fed beef steaks

To determine US consumer acceptance and value of beef from various countries, 24 taste panels of consumers (n = 273 consumers) were conducted in Denver and Chicago. Two pairs of strip steaks were evaluated for flavor, juiciness, tenderness, and overall acceptability on eight-point hedonic scales. One pair consisted of an Australian grass-fed strip steak and a domestic strip steak, whereas the other pair included Canadian and domestic strip steaks. The pairs were matched to similar Warner-Bratzler shear values and marbling scores to decrease variation associated with tenderness and juiciness. A variation of the Vickery auction was used to obtain silent, sealed bids on steaks (0.45 kg) from the same strip loins sampled in the taste panel. Consumers gave higher (P < 0.001) scores for flavor, juiciness, tenderness, and overall acceptability for domestic steaks compared with Australian grass-fed steaks. Domestic steaks averaged 3.68/0.45 dollars kg, whereas consumers placed an average value of 2.48/0.45 dollars kg on Australian grass-fed steaks (P < 0.001). Consumers rated Canadian steaks numerically lower for juiciness (P = 0.09) and lower (P < 0.005) for flavor, tenderness, and overall acceptability than domestic samples. Consumers placed an average value of 3.95/0.45 dollars kg for domestic steaks and 3.57/0.45 dollars kg for Canadian steaks (P < 0.01). Consumers (19.0%) who preferred Australian grass-fed steaks over domestic steaks paid 1.38/0.45 dollars kg more (P < 0.001), whereas consumers (29.3%) who favored the Canadian steaks over the domestic steaks paid 1.37/0.45 dollars kg more (P < 0.001) for the Canadian steaks. A majority of US consumers seem to be accustomed to the taste of domestic beef and prefer domestic steaks to beef from Australia grass-fed and Canadian beef.

Validity and reliability of a quantitative food frequency questionnaire measuring n-3 fatty acid intakes in cardiac patients in the Midwest: a validation pilot study

The purpose of this pilot study was to test the validity and reliability of a quantitative n-3 fatty acid food frequency questionnaire (FFQ) for later use with larger groups of individuals. A convenience sample of heart patients provided dietary data via three 24-hour food recalls and FFQs. Participants were women (n=17) and men (n=11), 43 to 77 years of age. The association of mean daily intake of n-3 fatty acids obtained using food recalls and the FFQ was assessed by Pearson correlation. The reliability of the FFQ was assessed using coefficient alpha. Correlation of n-3 fatty acid intake using the food recalls and the FFQ was r=0.42 (P<0.05). The coefficient alpha for the test-retest of the FFQ was .83. The top two foods, walnuts and flaxseed, contributed 58% of the n-3 fatty acid intake, and the third food, salmon, contributed 5%. This quantitative n-3 FFQ is a valid instrument for use in place of food recalls for estimating n-3 fatty acid intakes in heart patients and is a reliable instrument to estimate n-3 fatty acid intakes from plant, animal, and seafood sources. The FFQ should be tested in a larger population. Registered dietitians can use this FFQ to screen for intakes, educate patients on food sources, and measure change in intakes after nutrition intervention.