Improving estimates of population status and trend with superensemble models

Fishery managers must often reconcile conflicting estimates of population status and trend. Superensemble models, commonly used in climate and weather forecasting, may provide an effective solution. This approach uses predictions from multiple models as covariates in an additional “superensemble” model fitted to known data. We evaluated the potential for ensemble averages and superensemble models (ensemble methods) to improve estimates of population status and trend for fisheries. We fit four widely applicable data‐limited models that estimate stock biomass relative to equilibrium biomass at maximum sustainable yield (B/B_MSY). We combined these estimates of recent fishery status and trends in B/B_MSY with four ensemble methods: an ensemble average and three superensembles (a linear model, a random forest and a boosted regression tree). We trained our superensembles on 5,760 simulated stocks and tested them with cross‐validation and against a global database of 249 stock assessments. Ensemble methods substantially improved estimates of population status and trend. Random forest and boosted regression trees performed the best at estimating population status: inaccuracy (median absolute proportional error) decreased from 0.42 – 0.56 to 0.32 – 0.33, rank‐order correlation between predicted and true status improved from 0.02 – 0.32 to 0.44 – 0.48 and bias (median proportional error) declined from ?0.22 – 0.31 to ?0.12 – 0.03. We found similar improvements when predicting trend and when applying the simulation‐trained superensembles to catch data for global fish stocks. Superensembles can optimally leverage multiple model predictions; however, they must be tested, formed from a diverse set of accurate models and built on a data set representative of the populations to which they are applied.     

Modeling Landscape Vegetation Pattern in Response to Historic Land-use: A Hypothesis-driven Approach for the North Carolina Piedmont,USA

Current methods of vegetation analysis often assume species response to environmental gradients is homogeneously monotonic and unimodal. Such an approach can lead to unsatisfactory results, particularly when vegetation pattern is governed by compensatory relationships that yield similar outcomes for various environmental settings. In this paper we investigate the advantages of using classification tree models (CART) to test specific hypotheses of environmental variables effecting dominant vegetation pattern in the Piedmont. This method is free of distributional assumptions and is useful for data structures that contain non-linear relationships and higher-order interactions. We also compare the predictive accuracy of CART models with a parametric generalized linear model (GLM) to determine the relative strength of each predictive approach. For each method, hardwood and pine vegetation is modeled using explanatory topographic and edaphic variables selected based on historic reconstructions of patterns of land use. These include soil quality, potential soil moisture, topographic position, and slope angle. Predictive accuracy was assessed on independent validation data sets. The CART models produced the more accurate predictions, while also emphasizing alternative environmental settings for each vegetation type. For example, relic hardwood stands were found on steep slopes, highly plastic soils, or hydric bottomlands – alternatives not well captured by the homogeneous GLM. Our results illustrate the potential utility of this flexible modeling approach in capturing the heterogeneous patterns typical of many ecological datasets.     

Effects of passive transfer of immunity on results of diagnostic tests for antibodies against feline immunodeficiency virus in kittens born to vaccinated queens

OBJECTIVE: To determine whether passive transfer of immunity affects results of diagnostic tests for antibodies against FIV in kittens born to vaccinated queens. DESIGN: Experimental trial. ANIMALS: 12 specific-pathogen-free queens and their 55 kittens. PROCEDURE: Queens were vaccinated with a whole-virus FIV vaccine prior to breeding. Serum was obtained from the queens on the day of parturition and from the kittens on days 2 and 7, then weekly until results of tests for antibodies against FIV were negative for 2 consecutive weeks. Milk was collected from the queens daily for the first week and then weekly. Serum and milk were tested for antibodies against FIV with 2 commercial assays. RESULTS: Antibodies against FIV were detected in serum obtained from the queens on the day of parturition and in the milk throughout lactation. All kittens tested positive for antibodies against FIV at 2 days of age. At 8 weeks of age, 30 (55%) kittens tested positive with 1 of the commercial assays, and 35 (64%) tested positive with the other. All kittens tested negative for antibodies against FIV by 12 weeks of age. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that kittens readily absorb antibodies against FIV in colostrum from vaccinated queens and that these antibodies may interfere with results of commercially available tests for FIV infection past the age of weaning. Currently licensed diagnostic tests for FIV infection are unable to distinguish among kittens with antibodies against FIV as a result of infection, passive transfer from infected queens, and passive transfer from vaccinated queens.     

Comparison of myocardial contrast enhancement via cardiac magnetic resonance imaging in healthy cats and cats with hypertrophic cardiomyopathy

OBJECTIVE: To quantify myocardial contrast enhancement (MCE) of the left ventricle (LV) by use of cardiac magnetic resonance imaging (CMRI) in healthy cats and cats with hypertrophic cardiomyopathy (HCM) and to compare MCE between the 2 groups. ANIMALS: 10 healthy cats and 26 Maine Coon cats with moderate to severe HCM but without clinical evidence of congestive heart failure. PROCEDURE: Anesthetized cats underwent gradient echo CMRI examination. Short-axis images of the LV were acquired before and 7 minutes after IV administration of gadolinium dimeglumine. Regions of interest were manually traced in the quadrants of 5 mid-LV slices acquired at end systole, and the MCE percentage was calculated from summed weight-averaged data from all slices. Doppler tissue imaging echocardiography was performed to measure the early diastolic myocardial velocity (Em) as an index of diastolic function. Three-way repeated-measures ANOVA was used to determine differences in MCE between cats with HCM and healthy cats. Simple linear regression was used to assess whether MCE was correlated with LV mass, LV mass index (LVMI), or Em. A Student t test was used to compare the SDs of the postcontrast myocardial signal intensity between the 2 groups. RESULTS: There was no difference in MCE between cats with HCM and healthy cats. There was no correlation of MCE with LV mass, LVMI, or Em. There was no difference in heterogeneity of signal intensities of LV myocardium between the 2 groups. CONCLUSIONS AND CLINICAL RELEVANCE: Contrast-enhancement CMRI was not useful in detecting diffuse myocardial fibrosis in cats with HCM.     

Response of induced bone defects in horses to collagen matrix containing the human parathyroid hormone gene

OBJECTIVE: To determine whether human parathyroid hormone (hPTH) gene in collagen matrix could safely promote bone formation in diaphyseal or subchondral bones of horses. ANIMALS: 8 clinically normal adult horses. PROCEDURE: Amount, rate, and quality of bone healing for 13 weeks were determined by use of radiography, quantitative computed tomography, and histomorphometric analysis. Diaphyseal cortex and subchondral bone defects of metacarpi were filled with hPTH(1-34) gene-activated matrix (GAM) or remained untreated. Joints were assessed on the basis of circumference, synovial fluid analysis, pain on flexion, lameness, and gross and histologic examination. RESULTS: Bone volume index was greater for cortical defects treated with hPTH(1-34) GAM, compared with untreated defects. Bone production in cortical defects treated with hPTH(1-34) GAM positively correlated with native bone formation in untreated defects. In contrast, less bone was detected in hPTH(1-34) GAM-treated subchondral bone defects, compared with untreated defects, and histology confirmed poorer healing and residual collagen sponge. CONCLUSIONS AND CLINICAL RELEVANCE: Use of hPTH(1-34) GAM induced greater total bone, specifically periosteal bone, after 13 weeks of healing in cortical defects of horses. The hPTH(1-34) GAM impeded healing of subchondral bone but was biocompatible with joint tissues. Promotion of periosteal bone formation may be beneficial for healing of cortical fractures in horses, but the delay in onset of bone formation may negate benefits. The hPTH(1-34) GAM used in this study should not be placed in articular subchondral bone defects, but contact with articular surfaces is unlikely to cause short-term adverse effects.     

Atrial fibrillation in cats: 50 cases (1979-2002)

OBJECTIVE: To determine signalment, clinical signs, diagnostic findings, treatment, and outcome for cats with atrial fibrillation (AF). DESIGN: Retrospective study. ANIMALS: 50 cats. PROCEDURE: Medical records of cats that met criteria for a diagnosis of AF (ECG consisting of at least 2 leads, clear absence of P waves, supraventricular rhythm, and convincingly irregularly irregular rhythm) and had undergone echocardiography were reviewed. RESULTS: There were 41 males (37 castrated) and 9 females (7 spayed). Forty-one were of mixed breeding; 9 were purebred. Mean +/- SD age was 10.2 +/- 3.7 years. The most common chief complaints were dyspnea, aortic thromboembolism, and lethargy. In 11 cats, AF was an incidental finding. Mean +/- SD ventricular rate was 223 +/- 36 beats/min. The most common echocardiographic abnormalities were restrictive or unclassified cardiomyopathy (n = 19), concentric left ventricular hypertrophy (18), and dilated cardiomyopathy (6). Mean +/- SD left atrial-to-aortic diameter ratio (n = 39) was 2.55 +/- 0.80. The most common thoracic radiographic findings were cardiomegaly, pleural effusion, and pulmonary edema. Median survival time (n = 24) was 165 days (range, 0 to 1,095 days). Eight of 24 cats lived for > or = 1 year after a diagnosis of AF was made. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that AF occurs primarily in older adult male cats with structural heart disease severe enough to lead to atrial enlargement. Atrial fibrillation in these cats was most commonly first detected when signs of decompensated cardiac disease were evident, but also was commonly identified as an incidental finding.     

Salmonella,Campylobacter, Clostridium difficile,and anti‐microbial resistant Escherichia coli in the faeces of sympatric meso‐mammals in southern Ontario,Canada

The role of free‐ranging wildlife in the epidemiology of enteropathogens causing clinical illness in humans and domestic animals is unclear. Salmonella enterica and anti‐microbial resistant bacteria have been detected in the faeces of raccoons (Procyon lotor), but little is known about the carriage of these bacteria in other sympatric meso‐mammals. Our objectives were to: (a) report the prevalence of Salmonella and associated anti‐microbial resistance, Campylobacter spp, Clostridium difficile, and anti‐microbial resistant Escherichia coli in the faeces of striped skunks (Mephitis mephitis) and Virginia opossums (Didelphis virginiana) in southern Ontario; and (b) compare the prevalence of these bacteria in the faeces of these meso‐mammal hosts with raccoons from a previously reported study. Faecal swabs were collected from striped skunks and Virginia opossums on five swine farms and five conservation areas from 2011 to 2013. Salmonella was detected in 41% (9/22) and 5% (5/95) of faecal swabs from Virginia opossums and striped skunks, respectively. None of the Salmonella serovars carried resistance to anti‐microbials. The prevalence of Campylobacter spp., C. difficile, and anti‐microbial resistant E. coli ranged from 6% to 22% in striped skunk and Virginia opossums. Using exact logistic regression, Salmonella was significantly more likely to be detected in faecal swabs of Virginia opossums than skunks and significantly less likely in faecal swabs from skunks than raccoons from a previously reported study. In addition, Campylobacter spp. was significantly more likely to be detected in raccoons than opossums. Salmonella Give was detected in 8/9 (89%) of Salmonella‐positive Virginia opossum faecal swabs. Our results suggest that striped skunks and Virginia opossums have the potential to carry pathogenic enteric bacteria in their faeces. The high prevalence of Salmonella Give in Virginia opossum faecal swabs in this study as well as its common occurrence in other Virginia opossum studies throughout North America suggests Virginia opossums may be reservoirs of this serovar.     

Effect of oral supplementation of probiotic strains of Lactobacillus rhamnosus and Enterococcus faecium on the composition of the faecal microbiota of foals

Effects of probiotics on the intestinal microbiota of foals are yet insufficiently studied. The aim of this study was to investigate whether supplementation of Lactobacillus rhamnosus (DSM 7133) and Enterococcus faecium (DSM 7134) influences the bacterial composition of the faecal microbiota of foals. A total of 34 newborn foals were randomly assigned to the placebo group (PG, n = 16) and the treatment group (TG, n = 18). From day 1 to day 14 of life, foals orally received 3 ml of either a probiotic preparation (1.05 × 10⁹ CFU E. faecium and 4.50 × 10⁸ CFU L. rhamnosus) or placebo (carrier) once a day. Faeces were collected directly from the rectum immediately after birth (meconium) and at day 14 and day 56 of life. Samples of 12 foals per group were selected for microbiological analysis. DNA was extracted and used for polymerase chain reaction–denaturing gradient gel electrophoresis (PCR‐DGGE) and quantitative PCR. No DNA or amplicons were obtained from meconium. There were no differences in richness of bands and Shannon index of diversity regarding the Clostridium cluster XIVa between groups. Cluster analysis and principal coordinate analysis of DGGE data showed a clear effect of age. Band‐based similarity of bacterial clusters (Dice coefficient) decreased from day 14 to day 56 of life (p < 0.001) in PG foals only resulting in lower similarity in PG versus TG foals when 2 month old (p < 0.01). Five of thirty re‐amplified bands were identified on species level. Others were assigned either to family (mainly Lachnospiraceae) or genus level (Akkermansia). The bands related to Akkermansia muciniphila or Akkermansia spp. appeared almost in all DGGE profiles. Two‐week supplementation of the probiotic preparation to foals had no significant impact on the composition of the faecal microbiota but it appears to have prevented the reduction of bacterial similarity between 2 and 8 weeks of age observed in not treated foals.     

Basalt Milkvetch Responses to Novel Restoration Treatments in the Great Basin

The restoration of native forbs in the Great Basin and similar dryland ecosystems remains a great challenge for land managers. Variable soil water, precocious germination and emergence, and the presence of soil fungal pathogens often reduce plant establishment. Novel restoration treatments that increase soil water during early forb life stages, delay germination and emergence to coincide with favorable spring conditions, and reduce mortality from soil fungal pathogens may benefit native forb restoration. We compared the efficacy of three novel treatments—snow fencing, plant protection fabric, and seed coatings—to improve establishment of a forb species native to the Great Basin, basalt milkvetch (Astragalus filipes Torr. ex A. Gray). We replicated treatments plus a no-treatment control at three sites in the Great Basin in a randomized complete block design over 2 yr. To evaluate the efficacy of our restoration treatments, we measured germination, seedling emergence, establishment, and second-yr survival. The effects of snow fencing and plant protection fabric varied by site and life stage and were likely influenced by the wet spring conditions across sites, particularly the two northern sites. Snow fencing increased establishment and second-yr survival at one site. Plant protection fabric did not benefit any life stage at any site. Seed coatings increased seedling emergence at all sites but did not affect establishment or survival. Overall, second-yr survival remained low across all sites and treatments. Our study indicates that our treatments can positively affect basalt milkvetch emergence, establishment, and survival, but additional management actions are needed to improve long-term restoration success of native forbs.