Inferential implications of normalizing binomial proportions in a structural equation model: A simulation study motivated by feedlot data

Most commercial software for implementation of structural equation models (SEM) cannot explicitly accommodate outcome variables of binomial nature. As a result, SEM modeling strategies of binomial outcomes are often based on normal approximations of empirical proportions. Inferential implications of these approximations are particularly relevant to health-related outcomes. The objective of this study was to assess the inferential implications of specifying a binomial variable as an empirical proportion (%) in predictor and outcome roles in a SEM. We addressed this objective first by a simulation study, and second by a proof-of-concept data application on beef feedlot morbidity to bovine respiratory disease (BRD). We simulated data on body weight at feedlot arrival (AW), morbidity count for BRD (Mb), and average daily gain (ADG). Alternative SEMs were fitted to the simulated data. Model 1 specified a directed acyclic causal diagram with morbidity fitted as a binomial outcome (Mb) and as a proportion (Mb_p) predictor. Model 2 specified a similar causal diagram with morbidity fitted as a proportion for both outcome and predictor roles within the network. Structural parameters for Model 1 were accurately estimated based on the nominal coverage probability of 95 % confidence intervals. In turn, there was poor coverage for most morbidity-related parameters under Model 2. Both SEM models showed adequate empirical power (>80 %) to detect parameters not equal to zero. Model 1 and Model 2 produced predictions that were reasonable from a management standpoint, as determined by calculating the root mean squared error (RMSE) through cross-validation. However, interpretability of parameter estimates in Model 2 was impaired due to the model misspecification relative to the data generation. The data application fitted SEM extensions, Model 1 * and Model 2 * , to a dataset from a group of feedlots in the Midwestern US. Models 1 * and 2 * included explanatory covariates, specifically percent shrink (PS), backgrounding type (BG), and season (SEA). Lastly, we tested if AW exerted both direct and BRD-mediated indirect effects on ADG using Model 2 * . In Model 1 * , mediation was not testable due to the incomplete path from morbidity as a binomial outcome through Mb_p as a predictor to ADG. Model 2 * supported a minor morbidity-mediated mechanism between AW and ADG, though parameter estimates were not directly interpretable. Our results indicate normal approximation to a binomial disease outcome in a SEM may be a viable option for inference on mediation hypotheses and for predictive purposes, despite limitations in interpretability due to inherent model misspecification.

Describing capability, opportunity, and motivation for food safety practices among actors in the Cambodian informal vegetable market

Introduction

Several Cambodian initiatives seek to improve nutritional outcomes via increased production and consumption of nutrient-dense foods, including vegetables. However, food safety gaps in informal markets, where most vegetables are purchased, allow for the transmission of foodborne pathogens and threaten the positive nutritional outcomes associated with vegetable consumption.

Methods

This study describes a tool used to measure perceptions of Cambodians involved with informal vegetable markets regarding their capabilities, opportunities, and motivations to implement food safety practices. The quantitative tool could also be used to assess capability, opportunity, and motivation to adopt a behavior in a wide range of development contexts. To these ends, a questionnaire assessing these perceptions was developed using the Capability, Opportunity, Motivation-Behavior (COM-B) model of behavior and the Theoretical Domains Framework (TDF).

Results

The questionnaire was piloted with vegetable vendors in Phnom Penh (N = 55), revised, and subsequently implemented in the provinces of Battambang and Siem Reap with vegetable producers, distributors, and vendors (N = 181). Confirmatory factor analysis resulted in a nine-factor model corresponding to TDF constructs with a comparative fit index of 0.91, a Tucker-Lewis index of 0.89, and a root mean square error of ~0.05. Further analysis indicated that vegetable vendors and distributors typically had significantly higher (p < 0.05) levels of perceived motivation and capability to implement the target food safety practice (washing surfaces that come in contact with vegetables with soap and water every day) compared to their perceived opportunity to do so. Among farmers, however, levels of perceived motivation were significantly higher (p < 0.05) than levels of perceived opportunity and capability. In addition, vendors in Battambang had significantly higher (p < 0.05) levels of perceived capability, opportunity, and motivation to implement the target food safety practice in comparison to farmers in either province. Vendors in Battambang had significantly higher (p < 0.05) levels of perceived opportunity and motivation than vendors in Siem Reap.

Conclusions

These data suggest that efforts to bolster vegetable vendors' and distributors' perceived opportunity and vegetable farmers' perceived opportunity and capability to implement food safety practices could increase the likelihood of adoption of the target food safety practice.

Toceranib phosphate in the management of canine insulinoma: A retrospective multicentre study of 30 cases (2009-2019)

BACKGROUND

Insulinomas are the most common tumour of the endocrine pancreas in dogs. These malignant tumours have a high metastatic rate and limited chemotherapeutic options. The multi-receptor tyrosine kinase inhibitor sunitinib malate has benefit in the treatment of metastatic insulinoma in people. Toceranib phosphate, an analogous veterinary agent, may provide benefit for dogs.

METHODS

A retrospective study describing the extent and duration of clinical outcomes and adverse events (AEs) in dogs diagnosed with insulinoma and receiving toceranib.

RESULTS

Records for 30 dogs diagnosed with insulinoma and having received toceranib were identified from a medical record search of five university and eight referral hospitals. The median progression-free interval and overall survival time were 561 days (95% confidence interval (CI): [246, 727 days]) and 656 days (95% CI: [310, 1045 days]), respectively. Of the dogs for which the canine Response evaluation criteria for solid tumours tool could be applied, the majority (66.7%) showed either a complete response, partial response or stable disease. Time to clinical progression was associated with prior intervention and type of veterinary practice. Larger dogs were at increased risk for disease progression and death. No novel AEs were reported.

CONCLUSIONS

Most dogs diagnosed with insulinoma and receiving toceranib appeared to have a clinical benefit. Randomised, prospective studies are needed to better elucidate and objectively quantify the potential effect and survival benefit of toceranib therapy for management of insulinoma in dogs.

Investigating Salmonella enterica, Escherichia coli, and Coliforms on Fresh Vegetables Sold in Informal Markets in Cambodia†

ABSTRACT

Vegetables in Cambodia are commonly sold in informal markets lacking food safety standards and controls. Current data on microbial contamination of vegetables in Cambodian informal markets are limited. The purpose of this study was to investigate Salmonella enterica and indicator organisms (Escherichia coli and coliforms) on the surface of fresh vegetables sold in informal markets in Cambodia. Samples of loose-leaf lettuce, tomatoes, and cucumbers were collected from 104 vendors at four informal markets in Battambang and Siem Reap provinces during the rainy and dry seasons. Detection methods for S. enterica were adapted from the U.S. Food and Drug Administration's Bacteriological Analytical Manual. Coliform and E. coli populations were quantified by plating onto E. coli/coliform count plates. S. enterica was most prevalent on lettuce during the dry season (56.5%, 95% confidence interval [CI] [41.0, 70.8]) than during the rainy season (15.4%, 95% CI [7.5, 29.1]), whereas no significant seasonal differences were apparent for tomatoes and cucumbers. Regardless of season, levels of S. enterica were highest on lettuce (5.7 log CFU/g, 95% CI [5.5, 5.9]), relative to cucumbers (4.2 log CFU/g, 95% CI [3.8, 4.6]) and tomatoes (4.3 log CFU/g, 95% CI [4.1, 4.6]). For E. coli, prevalence was higher during the rainy season (34.0%, 95% CI [25.4, 43.8]) than during the dry season (9.1%, 95% CI [4.9, 16.5]), with the highest prevalence estimated on lettuce. Coliform levels on lettuce and tomatoes were greater during the rainy season (6.3 and 5.3 log CFU/g, 95% CI [5.7, 6.8] and [4.7, 5.8], respectively) than during the dry season (5.2 and 3.9 log CFU/g, 95% CI [4.7, 5.7] and [3.4, 4.4], respectively). These results indicate seasonal patterns for microbial prevalence in lettuce and an overall high level of bacterial contamination on raw vegetables sold in Cambodian informal markets.

HIGHLIGHTS

Prevalence of Salmonella enterica Isolated from Food Contact and Nonfood Contact Surfaces in Cambodian Informal Markets

ABSTRACT

The lack of hygiene and sanitation practices and insufficient infrastructure in Cambodian informal markets may increase the risk of food contamination, specifically raw vegetables, which in turn may increase the chances of contracting a foodborne disease. The aims of this study in informal markets in Cambodia were (i) to quantify the prevalence of Salmonella enterica based upon differences in season of the year (rainy versus dry), surface types (food contact surfaces versus nonfood contact surfaces), and location of vendors within the market (inside versus outside) and (ii) to characterize S. enterica serotype prevalence. A total of 310 samples were screened for S. enterica prevalence following the U.S. Department of Agriculture guidelines, and results were confirmed by PCR assay. Whole genome sequencing was used to determine the serotype for each isolate in silico using SeqSero 1.0 on draft genomes. A total of 78 samples were confirmed positive for S. enterica. During the dry season, S. enterica was more prevalent on food contact surfaces than on nonfood contact surfaces (estimated probability of detection [confidence interval]: 0.41 [0.25, 0.59] and 0.17 [0.08, 0.32], respectively; P = 0.002), but no differences were apparent in the rainy season. No differences in S. enterica prevalence were found based on location within the market (P = 0.61). Sixteen S. enterica serotypes were detected across multiple surfaces. The most common S. enterica serotypes were Rissen (18 isolates), Hvittingfoss (11), Corvallis (10), Krefeld (8), Weltevreden (6), and Altona (6). Accurate data on the prevalence of S. enterica in informal markets are crucial for the development of effective surveillance and implementation of suitable intervention strategies at the domestic level, thus preventing foodborne illness.

HIGHLIGHTS

Improved Accuracy of High-Throughput Phenotyping From Unmanned Aerial Systems by Extracting Traits Directly From Orthorectified Images

The development of high-throughput genotyping and phenotyping has provided access to many tools to accelerate plant breeding programs. Unmanned Aerial Systems (UAS)-based remote sensing is being broadly implemented for field-based high-throughput phenotyping due to its low cost and the capacity to rapidly cover large breeding populations. The Structure-from-Motion photogrammetry processes aerial images taken from multiple perspectives over a field to an orthomosaic photo of a complete field experiment, allowing spectral or morphological trait extraction from the canopy surface for each individual field plot. However, some phenotypic information observable in each raw aerial image seems to be lost to the orthomosaic photo, probably due to photogrammetry processes such as pixel merging and blending. To formally assess this, we introduced a set of image processing methods to extract phenotypes from orthorectified raw aerial images and compared them to the negative control of extracting the same traits from processed orthomosaic images. We predict that standard measures of accuracy in terms of the broad-sense heritability of the remote sensing spectral traits will be higher using the orthorectified photos than with the orthomosaic image. Using three case studies, we therefore compared the broad-sense heritability of phenotypes in wheat breeding nurseries including, (1) canopy temperature from thermal imaging, (2) canopy normalized difference vegetation index (NDVI), and (3) early-stage ground cover from multispectral imaging. We evaluated heritability estimates of these phenotypes extracted from multiple orthorectified aerial images via four statistical models and compared the results with heritability estimates of these phenotypes extracted from a single orthomosaic image. Our results indicate that extracting traits directly from multiple orthorectified aerial images yielded increased estimates of heritability for all three phenotypes through proper modeling, compared to estimation using traits extracted from the orthomosaic image. In summary, the image processing methods demonstrated in this study have the potential to improve the quality of the plant trait extracted from high-throughput imaging. This, in turn, can enable breeders to utilize phenomics technologies more effectively for improved selection.

Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains' climate gradient: Implications for climate change and restoration

Plant response to climate depends on a species' adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, and wet ecotypes originating from western KS to Illinois that span 500-1,200 mm rainfall/year. We aimed to answer: (a) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? (b) When planted in the homesite, is there a trait syndrome for each ecotype? (c) How are genotypes and phenotypes structured by climate? and (d) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in homesite, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass, and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated with primarily precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration.

Evaluation of diabetes mellitus regulation in dogs treated with ophthalmic preparations of prednisolone acetate versus diclofenac sodium

OBJECTIVE

To evaluate and compare regulation of diabetes mellitus (DM) in dogs with cataracts and well-controlled DM that received an ophthalmic preparation of prednisolone acetate versus diclofenac sodium.

ANIMALS

22 client-owned dogs with cataracts and well-controlled DM.

PROCEDURES

A prospective, randomized, double-masked, experimental study was conducted. On days 0 and 32, serum fructosamine concentrations (SFCs), clinical scores, and body weights were determined. Dogs were assigned to receive a topically administered ophthalmic preparation of either prednisolone acetate 1% or diclofenac sodium 0.1% in each eye 4 times daily for 28 days. Data analysis was conducted with generalized linear mixed models.

RESULTS

Findings indicated no meaningful differences in SFCs, clinical scores, or body weights between the treatment groups on days 0 or 32. Clinical score on day 0 was positively associated with SFC, as indicated by the corresponding rate of change such that each 1 -unit increase in clinical score was associated with an approximately 45.6 ± 9.4 μmol/L increase in SFC. In addition, the least squares mean ± SEM SFC was higher in spayed females (539.20 ± 19.23 μmol/L; n = 12) than in castrated males (458.83 ± 23.70 μmol/L; 8) but did not substantially differ between sexually intact males (446.27 ± 49.72 μmol/L; 2) and spayed females or castrated males regardless of the treatment group assigned.

CONCLUSIONS AND CLINICAL RELEVANCE

Findings indicated no evidence for any differential effect on DM regulation (assessed on the basis of SFCs, clinical scores, and body weights) in dogs treated topically with an ophthalmic preparation of prednisolone versus an ophthalmic preparation of diclofenac. Additional research investigating plasma concentrations of topically applied ophthalmic glucocorticoid medications is warranted. (Am J Vet Res 2019;80:1129-1135).

Toceranib phosphate in the treatment of canine thyroid carcinoma: 42 cases (2009-2018)

Thyroid carcinoma is the most common endocrine malignancy in dogs. Thyroidectomy and radiation therapy control local disease, yet are not always feasible, and efficacious medical therapies need to be identified. Toceranib phosphate has been reported to provide clinical benefit (CB) in dogs with thyroid carcinoma, while its role in treatment-naïve thyroid tumours has not been well-described. The objective of this study was to describe the use of toceranib in the management of thyroid carcinomas in dogs in both the naïve-disease and prior therapy- settings. A medical record search identified 42 dogs diagnosed with thyroid carcinoma and treated with toceranib, of which 26 and 16 dogs were in settings of naïve-disease and after prior therapy, respectively. Twenty-three (88.4%) and twelve (75%) dogs experienced CB in the naïve and prior therapy settings, respectively. The median [95% confidence interval] progression free interval (PFI) for dogs in the naïve and prior therapy settings were 206 [106,740] and 1015 [92,1015] days, respectively. The median overall survival time (OST) for dogs in the naïve and prior therapy settings were 563 [246,916] and 1082 [289,1894] days, respectively. Overall, the data provided no evidence for differences in overall PFI (P > .20) or OST (P = .15) between settings. However, when asymptomatic at the time of diagnosis, dogs in the naïve setting showed poorer survival prognosis (estimated hazard ratio 17.2 [1.8, 163]) relative to dogs in the prior therapy setting. This study characterizes PFI, OST and CB with minimal AE in dogs with thyroid carcinoma treated with toceranib in both the naïve and prior therapy settings.

Accuracy of oxygen delivery through bubble humidifiers and nasal catheters

OBJECTIVE

To evaluate the equipment used for nasal insufflation of oxygen and determine its accuracy.

STUDY DESIGN

Original study.

METHODS

Oxygen delivery assemblies consisting of a flowmeter, bubble humidifier, oxygen delivery tubing and nasal insufflation catheters were assembled. Single and double catheter assemblies were made for four sizes of nasogastric feeding tubes (3.5 Fr, 5.0 Fr, 8.0 Fr and 10.0 Fr) resulting in 64 individual assemblies. A gas flow analyzer measured oxygen flow at the tip of the nasal catheter assemblies and from the pressure relief valve (PRV) of the bubble humidifiers. Statistical analyses were conducted to assess the functionality of assemblies. For functional assemblies, the accuracy of oxygen flow relative to the prescribed flow settings was determined.

RESULTS

Catheter size was significantly associated with the functionality of assemblies. Probability (95% confidence interval) of 3.5 Fr, 5.0 Fr and 8.0 Fr assemblies being functional was estimated at 0.53 (0.14, 0.89), 0.83 (0.36, 0.98) and 0.98 (0.76, 0.99), respectively. All 10.0 Fr assemblies were functional. Functional assemblies, in general, consistently under-delivered the prescribed flow because a large portion of set flow was diverted through the bubble humidifier PRV.

CONCLUSIONS

Leaks through the PRV cause significant diversion of oxygen prior to it reaching the catheter tips. Smaller patients are particularly susceptible, as small catheters limit oxygen delivery creating proportionally greater leaks through the PRV.

CLINICAL RELEVANCE

It was not possible to accurately deliver oxygen because of leaks through the PRV. Targeting a specific outcome (e.g., oxyhemoglobin saturation > 94%, PaO₂ 80-120 mmHg; 11-16 kPa) and avoiding unnecessarily high fractions of inspired oxygen cannot be done if flow delivery cannot be accurately assured. One possible solution would be to use a bubble humidifier with a 6 psi PRV that does not leak prior to reaching the opening pressure.

Effect of Integrating the Entomopathogenic Fungus (Hypocreales: Cordycipitaceae) and the Rove Beetle (Coleoptera: Staphylinidae) in Suppressing Western Flower Thrips (Thysanoptera: Thripidae) Populations Under Greenhouse Conditions

Western flower thrips, Frankliniella occidentalis (Pergande), is a destructive insect pest in greenhouse production systems. Therefore, integrating the entomopathogenic fungus, Beauveria bassiana (Balsamo) Vuillemin, with the soil-dwelling rove beetle, Dalotia coriaria (Kraatz), targeting different aboveground and belowground life stages may help effectively manage western flower thrips populations. Two greenhouse experiments were conducted evaluating five treatments: 1) insecticides (spinosad, pyridalyl, chlorfenapyr, and abamectin), 2) B. bassiana, 3) D. coriaria, 4) B. bassiana and D. coriaria combination, and 5) water control. The estimated mean number of western flower thrips adults captured on yellow sticky cards was significantly lower for the insecticide treatment (mean range: 0-46 western flower thrips adults per yellow sticky card) than the B. bassiana and D. coriaria combination (0.3-105.1 western flower thrips per yellow card) over 8 wk. There were no significant differences in the final foliar damage ratings of chrysanthemum, Dendranthema × grandiflorum (Ramat.) Kitam., plants among the five treatments in experiment 1, but there were significant differences in experiment 2. In experiment 2, chrysanthemum plants across all treatments were not marketable due to western flower thrips feeding damage. Therefore, using B. bassiana and D. coriaria early in production should suppress population growth by targeting both foliar-feeding and soil-dwelling life stages of western flower thrips simultaneously.

Investigating causal biological relationships between reproductive performance traits in high-performing gilts and sows1

Efficient management of swine production systems requires understanding of complex reproductive physiological mechanisms. Our objective in this study was to investigate potential causal biological relationships between reproductive performance traits in high-producing gilts and sows. Data originated from a nutrition experiment and consisted of 200 sows and 440 gilts arranged in body weight blocks and randomly assigned to dietary treatments during late gestation at a commercial swine farm. Reproductive performance traits consisted of weight gain during late gestation, total number born and number born alive in a litter, born alive average birth weight, wean-to-estrous interval, and total litter size born in the subsequent farrowing. Structural equation models combined with the inductive causation algorithm, both adapted to a hierarchical Bayesian framework, were employed to search for, estimate, and infer upon causal links between the traits within each parity group. Results indicated potentially distinct reproductive networks for gilts and for sows. Sows showed sparse connectivity between reproductive traits, whereas the network learned for gilts was densely interconnected, suggesting closely linked physiological mechanisms in younger females, with a potential for ripple effects throughout their productive lifecycle in response to early implementation of tailored managerial interventions. Cross-validation analyses indicated substantial network stability both for the general structure and for individual links, though results about directionality of such links were unstable in this study and will need further investigation. An assessment of relative statistical power in sows and gilts indicated that the observed network discrepancies may be partially explained on a biological basis. In summary, our results suggest distinctly heterogeneous mechanistic networks of reproductive physiology for gilts and sows, consistent with physiological differences between the groups. These findings have potential practical implications for integrated understanding and differential management of gilts and sows to enhance efficiency of swine production systems.

Generalized additive mixed model on the analysis of total transport losses of market-weight pigs1

Transportation losses of market-weight pigs are an animal welfare concern, and result in direct economic impact for producers and abattoirs. Such losses are related to multiple factors including pig genetics, human handling, management, and weather conditions. Understanding the factors associated with total transport losses (TTL) is important to the swine industry because it can aid decision-making, and help in the development of transportation strategies to minimize the risk of losses. Hence, the objective of this study was to investigate factors associated with TTL on market-weight pigs in typically field conditions for Midwestern United States using a generalized additive mixed model (GAMM). The final quasi-binomial GAMM included the fixed (main and interactions) effects of abattoir of destination, type of driver, average market weight, distance traveled, wind speed, precipitation, and temperature-humidity index (THI), as well as the random effects of truck companies and the combination of site of origin and period of the year. Results indicate significant associations between TTL and the main effect of all explanatory variables (P < 0.05), except for wind speed and precipitation. Interactions of average market weight × abattoir, and wind speed × precipitation were also significant. A complex nonlinear relationship between TTL and model covariates were observed for distance traveled, THI, and interaction terms. This study showed that TTL of market-weight pigs are caused by a complex system involving multiple interacting factors, which can be potentially managed to mitigate the risk of losses. In addition, the GAMM showed to be a simple and flexible approach to model TTL because it can capture nonlinear relationships, handle non-normal data, and can potentially accommodate data structure.

Effects of Tylosin Administration Routes on the Prevalence of Antimicrobial Resistance Among Fecal Enterococci of Finishing Swine

Antibiotics can be administered orally or parenterally in swine production, which may influence antimicrobial resistance (AMR) development in gut bacteria. A total of 40 barrows and 40 gilts were used to determine the effects of tylosin administration route on growth performance and fecal enterococcal AMR. The antibiotic treatments followed Food and Drug Administration label directions and were as follows: (1) no antibiotic (CON), (2) 110 mg tylosin per kg feed for 21 d (IN-FEED), (3) 8.82 mg tylosin per kg body weight through intramuscular injection twice daily for the first 3 d of each week for 3 weeks (IM), and (4) 66 mg tylosin per liter of drinking water (IN-WATER). Antibiotics were administered during d 0 to 21 and all pigs were then fed the CON diet from d 21 to 35. Fecal samples were collected on d 0, 21, and 35. Antimicrobial susceptibility was determined by microbroth dilution method. No evidence of route × sex interaction (p > 0.55) was observed for growth performance. From d 0 to 21, pigs receiving CON and IN-FEED had greater (p < 0.05) average daily gain (ADG) than those receiving IM, with the IN-WATER group showing intermediate ADG. Pigs receiving CON had greater (p < 0.05) gain-to-feed ratio (G:F) than IM and IN-WATER, but were not different from pigs receiving IN-FEED. Overall, enterococcal isolates collected from pigs receiving IN-FEED or IM were more resistant (p < 0.05) to erythromycin and tylosin than CON and IN-WATER groups. Regardless of administration route, the estimated probability of AMR to these two antibiotics was greater on d 21 and 35 than on d 0. In summary, IM tylosin decreased ADG and G:F in finishing pigs, which may be because of a response to the handling during injection administration. Tylosin administration through injection and feed resulted in greater probability of enterococcal AMR to erythromycin and tylosin compared with in-water treatment.

Postpartum supplementation of fermented ammoniated condensed whey improved feed efficiency and plasma metabolite profile

Postpartum dietary supplementation of gluconeogenic precursors may improve the plasma metabolite profile of dairy cows, reducing metabolic disorders and improving lactation performance. The objective of this trial was to examine the effects of supplementation with fermented ammoniated condensed whey (FACW) postpartum on lactation performance and on profile of plasma metabolites and hormones in transition dairy cows. Individually fed multiparous Holstein cows were blocked by calving date and randomly assigned to control (2.9% dry matter of diet as soybean meal; n = 20) or FACW (2.9% dry matter of diet as liquid GlucoBoost, Fermented Nutrition, Luxemburg, WI; n = 19) dietary treatments. Treatments were offered from 1 to 45 d in milk (DIM). Cows were milked twice a day. Dry matter intake and milk yield were recorded daily and averaged weekly. Individual milk samples from 2 consecutive milkings were obtained once a week for component analysis. Rumen fluid was collected (n = 3 cows/treatment) at 4 time points per day at 7 and 21 DIM. Blood samples were collected within 1 h before feeding time for metabolite analysis and hyperketonemia diagnosis. Supplementation of FACW improved feed efficiency relative to control; this effect may be partially explained by a marginally significant reduction in dry matter intake from wk 3 to 7 for FACW-supplemented cows with no detected FACW-driven changes in milk yield, milk protein yield, and milk energy output compared with control. Also, there was no evidence for differences in intake of net energy for lactation, efficiency of energy use, energy balance, or body weight or body condition score change from calving to 45 DIM between treatments. Supplementation of FACW shifted rumen measures toward greater molar proportions of propionate and butyrate, and lesser molar proportions of acetate and valerate. Cows supplemented with FACW had greater plasma glucose concentrations in the period from 3 to 7 DIM and greater plasma insulin concentrations compared with control. Plasma nonesterified fatty acid and β-hydroxybutyrate concentrations were decreased in cows supplemented with FACW compared with control cows in the period from 3 to 7 DIM. These findings indicate that FACW may have improved the plasma metabolite profile immediately postpartum in dairy cows. Additionally, supplementation of FACW resulted in improved feed efficiency as accessed by measures of milk output relative to feed intake.

Conceptual framework for investigating causal effects from observational data in livestock

Understanding causal mechanisms among variables is critical to efficient management of complex biological systems such as animal agriculture production. The increasing availability of data from commercial livestock operations offers unique opportunities for attaining causal insight, despite the inherently observational nature of these data. Causal claims based on observational data are substantiated by recent theoretical and methodological developments in the rapidly evolving field of causal inference. Thus, the objectives of this review are as follows: 1) to introduce a unifying conceptual framework for investigating causal effects from observational data in livestock, 2) to illustrate its implementation in the context of the animal sciences, and 3) to discuss opportunities and challenges associated with this framework. Foundational to the proposed conceptual framework are graphical objects known as directed acyclic graphs (DAGs). As mathematical constructs and practical tools, DAGs encode putative structural mechanisms underlying causal models together with their probabilistic implications. The process of DAG elicitation and causal identification is central to any causal claims based on observational data. We further discuss necessary causal assumptions and associated limitations to causal inference. Last, we provide practical recommendations to facilitate implementation of causal inference from observational data in the context of the animal sciences.

Effects of chlortetracycline alone or in combination with direct fed microbials on nursery pig growth performance and antimicrobial resistance of fecal Escherichia coli

A total of 300 nursery pigs (initially 5.9 ± 0.05 kg BW) were used in a 42-d growth trial to evaluate the effects of feeding a therapeutic level of chlortetracycline (CTC) with or without direct fed microbials (DFM) on growth performance and antimicrobial resistance (AMR) of fecal Escherichia coli. CTC is a broad-spectrum in-feed antibiotic commonly used in the swine industry. Weaned pigs (~21 d of age) were allotted to pens based on initial BW and fed a common starter diet for 4 d. Pens were then blocked by BW and allotted to dietary treatments in a completely randomized block design. Dietary treatments were arranged in a 2 × 3 factorial consisting of combinations of CTC (none vs. 400 mg/kg from days 0 to 42) and DFM (0 vs. 0.05% DFM 1 vs. 0.05% DFM 2). Fecal samples were collected from three randomly selected pigs from each pen on days 0, 21, and 42 for E. coli isolation and AMR determination. Overall, pigs fed diets containing CTC had improved (P < 0.001) ADG, ADFI, and BW compared to those not fed CTC with no evidence for any effect of either DFM 1 or DFM 2. Regardless of CTC, inclusion of DFM 2 in diets improved (P < 0.05) ADFI from days 0 to 14 and on day 14 BW compared to diets that did not include DFM 2. The addition of CTC with or without DFMs to nursery pig diets increased (P < 0.05) the probability of AMR to tetracycline and ceftiofur of fecal E. coli isolates, but this resistance generally decreased (P < 0.05) over time. A decrease (P < 0.05) in AMR to ampicillin and tetracycline (TET) throughout the trial was observed, while resistance to ceftriaxone decreased (P < 0.020) from days 0 to 21 and increased from days 21 to 42 amongst dietary treatments regardless of CTC or DFM inclusion in the diet. A CTC × DFM × day interaction (P < 0.015) was observed for streptomycin, whereby from days 21 to 42 AMR increased in diets containing either CTC or DFM 1 alone, but the combination decreased resistance. There was no evidence for any effect of DFMs on AMR of fecal E. coli isolates to any other antibiotics evaluated. In conclusion, therapeutic levels of added CTC with or without DFM inclusion improved nursery pig performance, but increased AMR of fecal E. coli isolates to TET and ceftiofur. A moderate improvement in intake and day 14 BW was observed when DFM 2 was included in the diet with or without CTC, but, except for streptomycin, there was no evidence that added dietary DFMs affected resistance of fecal E. coli to antibiotics.

Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.

Standardized ileal digestible valine:lysine dose response effects in 25- to 45-kg pigs under commercial conditions

Two experiments were conducted to estimate the standardized ileal digestible valine:lysine (SID Val:Lys) dose response effects in 25- to 45-kg pigs under commercial conditions. In experiment 1, a total of 1,134 gilts (PIC 337 × 1050), initially 31.2 kg ± 2.0 kg body weight (BW; mean ± SD) were used in a 19-d growth trial with 27 pigs per pen and seven pens per treatment. In experiment 2, a total of 2,100 gilts (PIC 327 × 1050), initially 25.4 ± 1.9 kg BW were used in a 22-d growth trial with 25 pigs per pen and 12 pens per treatment. Treatments were blocked by initial BW in a randomized complete block design. In experiment 1, there were a total of six dietary treatments with SID Val at 59.0, 62.5, 65.9, 69.6, 73.0, and 75.5% of Lys and for experiment 2 there were a total of seven dietary treatments with SID Val at 57.0, 60.6, 63.9, 67.5, 71.1, 74.4, and 78.0% of Lys. Experimental diets were formulated to ensure that Lys was the second limiting amino acid throughout the experiments. Initially, linear mixed models were fitted to data from each experiment. Then, data from the two experiments were combined to estimate dose-responses using a broken-line linear ascending (BLL) model, broken-line quadratic ascending (BLQ) model, or quadratic polynomial (QP). Model fit was compared using Bayesian information criterion (BIC). In experiment 1, ADG increased linearly (P = 0.009) with increasing SID Val:Lys with no apparent significant impact on G:F. In experiment 2, ADG and ADFI increased in a quadratic manner (P < 0.002) with increasing SID Val:Lys whereas G:F increased linearly (P < 0.001). Overall, the best-fitting model for ADG was a QP, whereby the maximum mean ADG was estimated at a 73.0% (95% CI: [69.5, >78.0%]) SID Val:Lys. For G:F, the overall best-fitting model was a QP with maximum estimated mean G:F at 69.0% (95% CI: [64.0, >78.0]) SID Val:Lys ratio. However, 99% of the maximum mean performance for ADG and G:F were achieved at, 68% and 63% SID Val:Lys ratio, respectively. Therefore, the SID Val:Lys requirement ranged from73.0% for maximum ADG to 63.2% SID Val:Lys to achieve 99% of maximum G:F in 25- to 45-kg BW pigs.

Invited review: Reproducible research from noisy data: Revisiting key statistical principles for the animal sciences

Reproducible results define the very core of scientific integrity in modern research. Yet, legitimate concerns have been raised about the reproducibility of research findings, with important implications for the advancement of science and for public support. With statistical practice increasingly becoming an essential component of research efforts across the sciences, this review article highlights the compelling role of statistics in ensuring that research findings in the animal sciences are reproducible-in other words, able to withstand close interrogation and independent validation. Statistics set a formal framework and a practical toolbox that, when properly implemented, can recover signal from noisy data. Yet, misconceptions and misuse of statistics are recognized as top contributing factors to the reproducibility crisis. In this article, we revisit foundational statistical concepts relevant to reproducible research in the context of the animal sciences, raise awareness on common statistical misuse undermining it, and outline recommendations for statistical practice. Specifically, we emphasize a keen understanding of the data generation process throughout the research endeavor, from thoughtful experimental design and randomization, through rigorous data analysis and inference, to careful wording in communicating research results to peer scientists and society in general. We provide a detailed discussion of core concepts in experimental design, including data architecture, experimental replication, and subsampling, and elaborate on practical implications for proper elicitation of the scope of reach of research findings. For data analysis, we emphasize proper implementation of mixed models, in terms of both distributional assumptions and specification of fixed and random effects to explicitly recognize multilevel data architecture. This is critical to ensure that experimental error for treatments of interest is properly recognized and inference is correctly calibrated. Inferential misinterpretations associated with use of P-values, both significant and not, are clarified, and problems associated with error inflation due to multiple comparisons and selective reporting are illustrated. Overall, we advocate for a responsible practice of statistics in the animal sciences, with an emphasis on continuing quantitative education and interdisciplinary collaboration between animal scientists and statisticians to maximize reproducibility of research findings.

Estimating parametric phenotypes that determine anthesis date in Zea mays: Challenges in combining ecophysiological models with genetics

Ecophysiological crop models encode intra-species behaviors using parameters that are presumed to summarize genotypic properties of individual lines or cultivars. These genotype-specific parameters (GSP’s) can be interpreted as quantitative traits that can be mapped or otherwise analyzed, as are more conventional traits. The goal of this study was to investigate the estimation of parameters controlling maize anthesis date with the CERES-Maize model, based on 5,266 maize lines from 11 plantings at locations across the eastern United States. High performance computing was used to develop a database of 356 million simulated anthesis dates in response to four CERES-Maize model parameters. Although the resulting estimates showed high predictive value (R2 = 0.94), three issues presented serious challenges for use of GSP’s as traits. First (expressivity), the model was unable to express the observed data for 168 to 3,339 lines (depending on the combination of site-years), many of which ended up sharing the same parameter value irrespective of genetics. Second, for 2,254 lines, the model reproduced the data, but multiple parameter sets were equally effective (equifinality). Third, parameter values were highly dependent (p<10⁻⁶⁹¹⁹) on the sets of environments used to estimate them (instability), calling in to question the assumption that they represent fundamental genetic traits. The issues of expressivity, equifinality and instability must be addressed before the genetic mapping of GSP’s becomes a robust means to help solve the genotype-to-phenotype problem in crops.

Modeling the effects of standardized ileal digestible isoleucine to lysine ratio on growth performance of nursery pigs. Transl Anim Sci 2017;1:437-447. [PMID: 32704667 PMCID: PMC7204974 DOI: 10.2527/tas2017.0048]

Two experiments evaluated the effects of increasing standardized ileal digestible (SID) Ile:Lys ratio on growth performance of nursery pigs. In both experiments, dietary treatments consisted of 40, 44, 48, 52, 54, 58, or 63% SID Ile:Lys ratio. Diets were formulated using analyzed ingredient AA values and NRC (2012) SID coefficients. A combination of field peas and spray dried blood cells were used to ensure a low enough Ile diet concentration while minimizing the excess of Leu. The experiments consisted of 8 pens per dietary treatment with 5 pigs per pen for a total of 280 nursery pigs per experiment (Exp. 1: PIC 327 × 1,050, initially 6.7 ± 1.0 kg BW; Exp. 2: DNA 600 × 241, initially 6.0 ± 0.97 kg BW). Data were analyzed using mixed models with heterogeneous variance, where appropriate. The dose response was further characterized using quadratic polynomial (QP), broken-line linear (BLL), or broken-line quadratic (BLQ) functional forms. For Exp. 1, diets were initiated 6-d post-weaning and fed for 12-d followed by a common diet from d 12 to 28. From d 0 to 12, increasing dietary SID Ile:Lys ratio increased ADG (linear, P < 0.005) and ADFI (quadratic, P < 0.017) but G:F decreased (quadratic, P < 0.043). For ADG, the QP, BLL, and BLQ models resulted in maximum ADG at 64.7, 52.0, and 52.0 SID Ile:Lys ratios, respectively. For ADFI, the BLL breakpoint occurred at 50.6 and the QP predicted maximum ADFI at 56.2 SID Ile:Lys ratio. In Exp. 2, diets were initiated 6-d post-weaning for 7 pens and 3-d post-weaning for one heavier block and fed for 18-d followed by a common diet from d 18 to 32. From d 0 to 18, ADG and ADFI increased (quadratic, P < 0.016) with no evidence for difference in G:F as SID Ile:Lys ratio increased. For ADG, the QP and BLL had similar fit with breakpoints or maximums occurring at 58.3 and 51.8% SID Ile:Lys ratio, respectively. For ADFI, the BLQ breakpoint occurred at 52.0 SID Ile:Lys and the QP maximum ADFI at 57.2% SID Ile:Lys ratio. In conclusion, broken-line models reported maxima of 52.0% Ile:Lys ratio while quadratic models were as high as 64% of Lys to maximize ADG and ADFI of 6- to 11-kg nursery pigs. However, for the QP models 99% of the maximum response was achieved with a dose comparable to that from the broken line models. Therefore, these results are similar to the NRC (2012) requirement estimate of 51.1 Ile:Lys ratio.

Modeling the effects of standardized ileal digestible valine to lysine ratio on growth performance of nursery pigs. Transl Anim Sci 2017;1:448-457. [PMID: 32704668 PMCID: PMC7204984 DOI: 10.2527/tas2017.0049]

Two experiments evaluated the effects of increasing Lys and Val on growth performance of nursery pigs. In Exp. 1,300 nursery pigs (PIC 327 × 1,050, initially 6.7 ± 1.4 kg BW) were randomly allotted to 1 of 6 diets containing 1.10, 1.20, 1.30, 1.40, 1.50, or 1.60% standardized ileal digestible (SID) Lys, with 10 pens per dietary treatment and 5 pigs per pen. Linear and nonlinear mixed models were fitted to estimate dose responses. From d 0 to 14, and for the overall 28 d period, ADG and G:F increased (linear, P < 0.001) as SID Lys increased, with no evidence of differences in ADFI. Dose response modeling indicated the SID Lys requirement for ADG and G:F was at 1.45% using a broken line linear (BLL) and greater than 1.60% using a quadratic polynomial (QP) model. In Exp. 2, 280 nursery pigs (PIC 327 × 1,050, initially 6.5 ± 1.3 kg BW) were allotted to 1 of 7 diets containing SID Val:Lys ratios of 50, 57, 63, 68, 73, 78, or 85%. The dietary SID Lys concentration 1.24% SID Lys which was below the estimated requirement from Exp. 1 and ensured the Val:Lys ratio was not underestimated. From d 0 to 14, ADG, ADFI, and G:F increased (quadratic, P < 0.039) with increasing SID Val:Lys. For ADG, the best fitting model was a BLL, with a breakpoint estimate of 62.9% SID Val:Lys [52.2, 73.7] ratio while for G:F the best fit model was a quadratic polynomial with a maximum G:F at 71.7% SID Val:Lys (95%CI:[58, > 85]). Average daily feed intake was also modeled with a quadratic polynomial and maximized at 73.7% Val:Lys (95% CI: [61, > 85]). In conclusion, the Val requirement ranged from approximately 63 to 74% of Lys depending on the response criteria modeled.

Implementing structural equation models to observational data from feedlot production systems

The objective of this study was to illustrate the implementation of a mixed-model-based structural equation modeling (SEM) approach to observational data in the context of feedlot production systems. Different from traditional multiple-trait models, SEMs allow assessment of potential causal interrelationships between outcomes and can effectively discriminate between direct and indirect effects. For illustration, we focused on feedlot performance and its relationship to health outcomes related to Bovine Respiratory Disease (BRD), which accounts for approximately 75% of morbidity and 50-80% of deaths in feedlots. Our data consisted of 1430 lots representing 178,983 cattle from 9 feedlot operations located across the US Great Plains. We explored functional links between arrival weight (AW; i = 1), BRD-related treatment costs (Trt$; as a proxy for health; i = 2) and average daily weight gain (ADG; as an indicator of productive performance i = 3), accounting for the fixed effect of sex and correlation patterns due to the clustering of lots within feedlots. We proposed competing plausible causal models based on expert knowledge. The best fitting model selected for inference supported direct effects of AW on ADG as well as indirect effects of AW on ADG mediated by Trt$. Direct effects from outcome i' to outcome i are quantified by the structural coefficient λ_ii', such that every unit increase in kg/head of AW had a direct effect of increasing ADG by approximately (estimate ± standard error) λˆ₃₁=0.002±0.0001 kg/head/day and also a direct effect of reducing Trt$ by an estimated λˆ₂₁=$0.08±0.006 USD per head. In addition, every $1 USD spent on Trt$ directly decreased ADG by an estimated λˆ₃₂=0.004±0.0006 kg/head/day. From these estimates, we show how to compute the indirect, Trt$-mediated, effect of AW on ADG, as well as the overall effect of AW on ADG, including both direct and indirect effects. We further compared estimates of SEM-based effects with those obtained from standard linear regression mixed models and demonstrated the additional advantage of explicitly distinguishing direct and indirect components of an overall regression effect using SEMs. Understanding the direct and indirect mechanisms of interplay between health and performance outcomes may provide valuable insight into production systems.

Effect of cleaning status on accuracy and precision of oxygen flowmeters of various ages

OBJECTIVE

To evaluate oxygen flowmeters for accuracy and precision, assess the effects of cleaning and assess conformity to the American Society for Testing Materials (ASTM) standards.

STUDY DESIGN

Experimental study.

METHODS

The flow of oxygen flowmeters from 31 anesthesia machines aged 1-45 years was measured before and after cleaning using a volumetric flow analyzer set at 0.5, 1.0, 2.0, 3.0, and 4.0 L minute^-1. A general linear mixed models approach was used to assess flow accuracy and precision.

RESULTS

Flowmeters 1 year of age delivered accurate mean oxygen flows at all settings regardless of cleaning status. Flowmeters ≥5 years of age underdelivered at flows of 3.0 and 4.0 L minute^-1. Flowmeters ≥12 years underdelivered at flows of 2.0, 3.0 and 4.0 L minute^-1 prior to cleaning. There was no evidence of any beneficial effect of cleaning on accuracy of flowmeters 5-12 years of age (p > 0.22), but the accuracy of flowmeters ≥15 years of age was improved by cleaning (p < 0.05). Regardless of age, cleaning increased precision, decreasing flow variability by approximately 17%. Nine of 31 uncleaned flowmeters did not meet ASTM standards. After cleaning, a different set of nine flowmeters did not meet standards, including three that had met standards prior to cleaning.

CONCLUSIONS

Older flowmeters were more likely to underdeliver oxygen, especially at higher flows. Regardless of age, cleaning decreased flow variability, improving precision. However, flowmeters still may fail to meet ASTM standards, regardless of cleaning status.

CLINICAL RELEVANCE

Cleaning anesthesia machine oxygen flowmeters improved precision for all tested machines and partially corrected inaccuracies in flowmeters ≥15 years old. A notable proportion of flowmeters did not meet ASTM standards. Cleaning did not ensure that they subsequently conformed to ASTM standards. We recommend annual flow output validation to identify whether flowmeters are acceptable for continued clinical use.

Effects of amino acids and energy intake during late gestation of high-performing gilts and sows on litter and reproductive performance under commercial conditions

The objective of this study was to determine the effects of AA and energy intake during late gestation on piglet birth weight and reproductive performance of high-performing (14.5 total born) gilts and sows housed under commercial conditions. At d 90 of gestation, a total of 1,102 females (PIC 1050) were housed in pens by parity group (gilts or sows) with approximately 63 gilts and 80 sows in each pen, blocked by BW within each pen, and each female was randomly assigned to dietary treatments within BW block. Dietary treatments consisted of combinations of 2 standardized ileal digestible (SID) AA intakes (10.7 or 20.0 g/d SID Lys and other AA met or exceeded the NRC [2012] recommendations) and 2 energy intakes (4.50 or 6.75 Mcal/d intake of NE) in a 2 × 2 factorial arrangement. Data were analyzed using generalized linear mixed models specified to recognize pen as the experimental unit for parity and the individual female as the experimental unit for dietary treatments. Results indicate an overall positive effect of high energy intake on BW gain during late gestation, although this effect was more manifest under conditions of high, as opposed to low, AA intake (interaction, < 0.001). Furthermore, the magnitude of BW gain response to increased energy intake was greater ( < 0.001) for sows compared with gilts. Sows fed high energy intake had a reduced probability of piglets born alive ( < 0.004) compared with those fed low energy, but no evidence for differences was found in gilts. This can be explained by an increased probability ( = 0.002) of stillborns in sows fed high energy intake vs. sows fed low energy intake. There were no evidences for differences among dietary treatments in litter birth weight and individual piglet birth weight of total piglets born. However, individual born alive birth weight was approximately 30 ± 8.2 g heavier ( = 0.011) for females fed high, as opposed to low, energy intake. Furthermore, piglets born alive were approximately 97 ± 9.5 g heavier ( < 0.001) for sows than for gilts. Preweaning mortality was decreased ( = 0.034) for females fed high AA intake compared with females fed low AA intake regardless of energy level. In conclusion, 1) BW gain of gilts and sows depended not only on energy but also on AA intake, 2) sows fed increased amount of energy had an increased stillborn rate, and 3) increased energy intake during late gestation had a positive effect on individual piglet birth weight with no evidence for such an effect for AA intake.

Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

BACKGROUND

Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on transcripts characterized by a small number of read counts, so-called low-count transcripts, as motivated by an ecological application in prairie grasses. Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Relative to big bluestem, sand bluestem exhibits qualitative phenotypic divergence consistent with enhanced drought tolerance, plausibly associated with transcripts of low expression levels. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60% of which are classified as low-count) collected from leaf tissue of individual plants of big bluestem (n = 4) and sand bluestem (n = 4). Focused on low-count transcripts, we compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the inferential performance of recently developed statistical methods for DE analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively.

RESULTS

Both DE methods seemed to properly control family-wise type 1 error on low-count transcripts, whereas edgeR robust showed greater power and DESeq2 showed greater precision and accuracy. However, specification of the degree of freedom parameter under edgeR robust had a non-trivial impact on inference and should be handled carefully. When properly specified, both DE methods showed overall promising inferential performance on low-count transcripts, suggesting that ad-hoc data filtering steps at arbitrary expression thresholds may be unnecessary. A note of caution is in order regarding the approximate nature of DE tests under both methods.

CONCLUSIONS

Practical recommendations for DE inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications focused on transcripts of low expression levels.

Tallman lettering as a strategy for differentiation in look-alike, sound-alike drug names: the role of familiarity in differentiating drug doppelgangers

Tallman lettering, capitalizing the dissimilar portions of easily confused drug names, is one strategy for reducing medication errors. We assessed the efficacy of Tallman lettering in a visually complex environment using a change detection method with healthcare providers and laypeople. In addition, the effect of familiarity with the drug name was assessed using a subset of responses collected from healthcare providers. Both healthcare providers and laypeople detected changes in confusable pairs of drug names more often (P < 0.0001) and more quickly (P < 0.05) when changes were presented in Tallman lettering, though the benefits were more pronounced for healthcare providers (p < 0.05). Familiarity with both drug names in a confusable pair mitigated the benefit of Tallman lettering. Results are discussed in terms of bottom-up and top-down attentional systems for processing of information in the context of the varied healthcare environments.

Evaluation of three point-of-care meters and a portable veterinary chemistry analyzer for measurement of blood glucose concentrations in black-tailed prairie dogs (Cynomys ludovicianus)

OBJECTIVE

To compare blood glucose concentrations of black-tailed prairie dogs (Cynomys ludovicianus) measured by use of a variety of portable analyzers with results from a laboratory biochemistry analyzer.

SAMPLE

Venous blood samples (3 mL) obtained from each of 16 healthy black-tailed prairie dogs.

PROCEDURES

A portion of each blood sample was used to measure glucose concentrations by use of an amperometric human point-of-care glucometer and a colorimetric species-specific portable blood glucose meter designed for veterinary use with both canine (code 5) and feline (code 7) settings. The remainder of each blood sample was placed into 2 tubes (one contained lithium heparin and the other contained no anticoagulant). A portable veterinary chemistry analyzer (PVCA) and a handheld analyzer were used to measure glucose concentration in heparinized blood. Serum glucose concentration was measured in the remaining portion by use of a biochemistry analyzer. A general linear mixed models approach was used to compare glucose concentrations and measurement bias obtained with the various measurement methods.

RESULTS

Measurement bias and differences in mean glucose concentrations were apparent with all measurement methods. In particular, the veterinary glucometer, whether used on the canine or feline setting, overestimated mean glucose concentrations, whereas the human glucometer, PVCA, and handheld analyzer underestimated mean glucose concentrations relative to the concentration obtained with the biochemistry analyzer.

CONCLUSIONS AND CLINICAL RELEVANCE

Results indicated that none of the measurement methods provided consistently accurate blood glucose concentrations of black-tailed prairie dogs, compared with values determined with a biochemistry analyzer.

To See or Not to See: Do Front of Pack Nutrition Labels Affect Attention to Overall Nutrition Information?

BACKGROUND

Front of pack (FOP) nutrition labels are concise labels located on the front of food packages that provide truncated nutrition information. These labels are rapidly gaining prominence worldwide, presumably because they attract attention and their simplified formats enable rapid comparisons of nutritional value.

METHODS

Eye tracking was conducted as US consumers interacted with actual packages with and without FOP labels to (1) assess if the presence of an FOP label increases attention to nutrition information when viewers are not specifically tasked with nutrition-related goals; and (2) study the effect of FOP presence on consumer use of more comprehensive, traditional nutrition information presented in the Nutritional Facts Panel (NFP), a mandatory label for most packaged foods in the US.

RESULTS

Our results indicate that colored FOP labels enhanced the probability that any nutrition information was attended, and resulted in faster detection and longer viewing of nutrition information. However, for cereal packages, these benefits were at the expense of attention to the more comprehensive NFP. Our results are consistent with a potential short cut effect of FOP labels, such that if an FOP was present, participants spent less time attending the more comprehensive NFP. For crackers, FOP labels increased time spent attending to nutrition information, but we found no evidence that their presence reduced the time spent on the nutrition information in the NFP.

CONCLUSIONS

The finding that FOP labels increased attention to overall nutrition information by people who did not have an explicit nutritional goal suggests that these labels may have an advantage in conveying nutrition information to a wide segment of the population. However, for some food types this benefit may come with a short-cut effect; that is, decreased attention to more comprehensive nutrition information. These results have implications for policy and warrant further research into the mechanisms by which FOP labels impact use of nutrition information by consumers for different foods.

Front of Pack Labels Enhance Attention to Nutrition Information in Novel & Commercial Brands

OBJECTIVES

1) To assess whether Front-of-Pack (FOP) nutrition labels garner attention more readily than more complete, mandated nutrition information (the Nutrition Facts Panel (NFP), required in the US), and 2) To determine whether label design characteristics, specifically, color coding and/or coding with facial icons, increase attention to the FOP label.

METHODS

In two experiments, we tracked the allocation of attention while participants (n=125) viewed novel and commercial packages with varied FOP designs using a change detection methodology.

RESULTS

We found empirical evidence that FOP labels are attended more often, and earlier, than the currently mandated NFP, and that this benefit is due both to its placement on the front of the package and to the design characteristics of the FOP. Specifically, the use of color in FOPs increased attention to the label, but there was no evidence that coding information via facial icons impacted attention.

CONCLUSIONS

Our work supports a growing body of evidence supporting the use of FOP labels to attract attention to nutritional information. Findings may be relevant to inform policy decisions on labeling standards.

Insecticide Rotation Programs with Entomopathogenic Organisms for Suppression of Western Flower Thrips (Thysanoptera: Thripidae) Adult Populations under Greenhouse Conditions

Western flower thrips, Frankliniella occidentalis (Pergande), is one of the most destructive insect pests of greenhouse production systems with the ability to develop resistance to a wide variety of insecticides. A common resistance management strategy is rotating insecticides with different modes of action. By incorporating entomopathogenic organisms (fungi and bacteria), which have discrete modes of action compared to standard insecticides, greenhouse producers may preserve the effectiveness of insecticides used for suppression of western flower thrips populations. The objective of this study was to determine how different rotation programs that include entomopathogenic organisms (Beauveria bassiana, Isaria fumosoroseus, Metarhizium anisopliae, and Chromobacterium subtsugae) and commonly used standard insecticides (spinosad, chlorfenapyr, abamectin, and pyridalyl) may impact the population dynamics of western flower thrips adult populations by means of suppression. Eight-week rotation programs were applied to chrysanthemum, Dendranthema x morifolium plants and weekly counts of western flower thrips adults captured on yellow sticky cards were recorded as a means to evaluate the impact of the rotation programs. A final quality assessment of damage caused by western flower thrips feeding on foliage and flowers was also recorded. Furthermore, a cost comparison of each rotation program was conducted. Overall, insecticide rotation programs that incorporated entomopathogenic organisms were not significantly different than the standard insecticide rotation programs without entomopathogenic organisms in suppressing western flower thrips adult populations. However, there were no significant differences among any of the rotation programs compared to the water control. Moreover, there was no differential effect of the rotation programs on foliage and flower quality. Cost savings of up to 34% (in US dollars) are possible when including entomopathogenic organisms in the rotation program. Therefore, by incorporating entomopathogenic organisms into insecticide rotation programs, greenhouse producers can decrease costs without affecting suppression, as well as diminish selection pressure on western flower thrips adult populations, which may avoid or delay resistance development.

Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains' precipitation gradient: implications for grassland restoration with climate change

Identifying suitable genetic stock for restoration often employs a 'best guess' approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations.

Characterisation of immune responses in healthy foals when a multivalent vaccine protocol was initiated at age 90 or 180 days

REASONS FOR PERFORMING STUDY

Protection from infectious disease requires antigen-specific immunity. In foals, most vaccine protocols are delayed until 6 months to avoid maternal antibody interference. Susceptibility to disease may exist prior to administration of vaccination at age 4-6 months.

OBJECTIVES

The aim of this investigation was to characterise immune activation among healthy foals in response to a multivalent vaccine protocol and compare immune responses when foals were vaccinated at age either 90 or 180 days.

STUDY DESIGN

Randomised block design.

METHODS

Twelve healthy foals with colostral transfer were blocked for age and randomly assigned to vaccination at age 90 days (treatment) or at age 180 days (control). Vaccination protocols included a 3-dose series and booster vaccine administered at age 11 months.

RESULTS

Immune response following vaccination at age 90 or 180 days was comparable for several measures of cellular immunity. Antigen specific CD4+ and CD8+ expression of interleukin-4, interferon-γ and granzyme B to eastern equine encephalomyelitis, western equine encephalomyelitis, West Nile virus, tetanus toxoid, equine influenza and equine herpesvirus-1/4 antigens were evident for both groups 30 days after initial vaccine and at age 344 days. Both groups showed a significant increase in antigen-specific immunoglobulin G expression following booster vaccine at age 11 months, thereby indicating memory immune responses.

CONCLUSIONS

The data presented in this report demonstrate that young foals are capable of immune activation following a 3-dose series with a multivalent vaccine, despite presence of maternal antibodies. Although immune activation does not automatically confer protection, several of the immune indicators measured showed comparable expression in foals vaccinated at 3 months relative to control foals vaccinated at age 6 months. In high-risk situations where immunity may be required earlier than following a conventional vaccine series, our data provide evidence that foals respond to immunisation initiated at 3 months in a comparable manner to foals initiated at an older age.

Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour-joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within-prairie genetic diversity (92%). Using Bayenv2, 14 top-ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScanFST outliers were in common with Bayenv2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.

Discrepancies in identification of left atrial enlargement using left atrial volume versus left atrial-to-aortic root ratio in dogs

Background

Left atrial size is prognostically important in dogs with myxomatous mitral valve disease (MMVD).

Hypothesis/Objectives

To compare the level of agreement in identification of left atrial enlargement (LAE) between the left atrial‐to‐aortic root ratio (LA : Ao) and left atrial volume using the biplane area‐length method indexed to body weight (LA Vol/BW).

Animals

Sixty dogs with MMVD and 22 normal dogs were prospectively studied with 2‐dimensional echocardiography.

Methods

The upper limit of normal for LA Vol/BW was defined as 1.1 mL/kg. LA : Ao was deemed normal if ≤1.5. To define overall disease severity, each dog was assigned a mitral regurgitation severity score (MRSS) based on echocardiographic parameters that did not include left atrial size. ACVIM staging also was utilized.

Results

Of 60 affected dogs, 20 were ACVIM Stage B1, 25 were Stage B2, and 15 were Stage C. LA Vol/BW identified LAE in 12 cases in which LA : Ao was normal; 7 of these were Stage B1 and 5 were Stage B2. This diagnostic disagreement was significant (P = .00012). Of the 12 cases in which diagnostic discrepancies were identified, 5/5 of the B2 dogs and 3/7 B1 dogs had a moderate MRSS, whereas 4/7 B1 dogs had a mild MRSS. No diagnostic discrepancies between LA : Ao and LA Vol/BW were apparent in dogs with a severe MRSS.

Conclusions and Clinical Importance

This study shows evidence of diagnostic disagreement between LA : Ao and LA Vol/BW for assessment of LAE. LA Vol/BW may be superior to LA : Ao for identification of mild LAE.

Field study of the comparative efficacy of gamithromycin and tulathromycin for the treatment of undifferentiated bovine respiratory disease complex in beef feedlot calves

OBJECTIVE

To compare the efficacy of gamithromycin with that of tulathromycin for the treatment of undifferentiated bovine respiratory disease complex (BRDC) in feedlot calves.

ANIMALS

1,049 weaned crossbred beef calves.

PROCEDURES

At each of 6 feedlots, newly arrived calves with BRDC were administered a single dose of gamithromycin (6.0 mg/kg, SC; n = 523) or tulathromycin (2.5 mg/kg, SC; 526). Case-fatality and BRDC retreatment rates during the first 120 days after treatment, final body weight, and average daily gain (ADG), were compared between treatments. At 2 feedlots, calves were assigned clinical scores for 10 days after treatment to determine recovery rates for each treatment. Bioequivalence limits for gamithromycin and tulathromycin were calculated for outcomes for which there was no significant difference between treatments.

RESULTS

Mean BRDC retreatment rate (17.7%) for calves administered gamithromycin was greater than that (9.0%) for calves administered tulathromycin. Mean case-fatality rate, final body weight, ADG, and clinical score 10 days after treatment did not differ significantly between treatments. Limits for mean differences within which gamithromycin was bioequivalent to tulathromycin were ± 2.4% for case-fatality rate, ± 13 kg for final body weight, and ± 0.1 kg/d for ADG.

CONCLUSIONS AND CLINICAL RELEVANCE

Calves administered gamithromycin had a higher BRDC retreatment rate than did calves administered tulathromycin; otherwise, the clinical efficacy did not differ between the 2 treatments for the treatment of BRDC in feedlot calves.

Effects of oxygen insufflation rate, respiratory rate, and tidal volume on fraction of inspired oxygen in cadaveric canine heads attached to a lung model

OBJECTIVE

To assess the effects of oxygen insufflation rate, respiratory rate, and tidal volume on fraction of inspired oxygen (Fio2) in cadaveric canine heads attached to a lung model.

SAMPLE

16 heads of canine cadavers.

PROCEDURES

Each cadaver head was instrumented with a nasal insufflation catheter through which oxygen was delivered. The trachea was attached to a sample collection port connected by means of corrugated tubing to a lung model. Eight treatment combinations that varied in respiratory rate (10 or 20 breaths/min), tidal volume (10 or 15 mL/kg), and oxygen insufflation rate (50 or 100 mL/kg/min) were applied to each head in a replicated Latin square design. Gas samples were manually collected, and inspired oxygen concentrations were analyzed. The Fio2 and end-tidal CO2 concentration were determined and compared among sample groups.

RESULTS

Estimated least squares mean Fio2 for various treatment combinations ranged from 32.2% to 60.6%. The Fio2 was significantly increased at the higher insufflation rate (estimated marginal least squares mean, 48.7% vs 38.6% for 100 and 50 mL/kg/min, respectively), lower respiratory rate (48.9% vs 38.3% for 10 and 20 breaths/min, respectively), and smaller tidal volume (46.8% vs 40.0% for 10 and 15 mL/kg, respectively).

CONCLUSIONS AND CLINICAL RELEVANCE

-Fio2 in the model was affected by oxygen insufflation rate, respiratory rate, and tidal volume. This information may potentially help clinicians interpret results of blood gas analysis and manage canine patients receiving oxygen insufflation via a nasal catheter.

Effect of castration method on neurohormonal and electroencephalographic stress indicators in Holstein calves of different ages

As public concern for food animal welfare increases, a need to validate objective pain assessment tools exists in order to formulate animal welfare policies and facilitate regulatory approval of compounds to alleviate pain in livestock in the United States. The aims of this study were (1) to compare the physiological response to pain induced by surgical and nonsurgical (band) castration in calves and (2) to elucidate age-related differences in pain response of calves subjected to different castration methods. Seventy-six Holstein bull calves were blocked by age (≤8-wk and ≥6-mo-old) and randomly assigned to 1 of 4 treatment groups: control (n=20), castration by banding (n=18), cut-and-clamp surgical castration (n=20), and cut-and-pull surgical castration (n=18). Measurements included electroencephalogram, heart rate variability, infrared thermography, electrodermal activity, and concentrations of serum cortisol and plasma substance P before, during, and within 20min following castration. Electroencephalogram recordings showed desynchronization for all treatments, consistent with increased arousal; yet the magnitude of desynchronization was greatest for 6-mo-old calves castrated by cut-and-clamp. Additionally, older calves in the cut-and-pull group showed greater desynchronization than younger calves in the same group. Based on the heart rate variability analysis, 6-mo-old calves in the control or cut-and-pull castration groups showed greater sympathetic tone than younger calves in the same treatment groups. Overall, younger calves showed lower electrodermal activity than older calves. Regardless of treatment, concentrations of cortisol and plasma substance P were greater in 6-mo-old calves relative to their younger counterparts, indicating a more robust response to all treatments in older calves. In summary, neurohormonal and electroencephalographic stress responses of calves to castration were age-specific. Castration by cut-and-clamp showed the most pronounced stress response in 6-mo-old calves. These findings provide evidence that support welfare policies recommending castration at an early age and the use of analgesic compounds at the time of surgical castration especially in older calves. However, the potential long-term negative consequences of early untreated pain must be considered and warrant further investigation.