Bayesian estimation in veterinary pharmacology:A conceptual and practical introduction

Sophisticated mathematical and computational tools have become widespread and important in veterinary pharmacology. Although the theoretical basis and practical applications of these have been widely explored in the literature, statistical inference in the context of these models has received less attention. Optimization methods, often with frequentist statistical inference, have been predominant. In contrast, Bayesian statistics have not been widely applied, but offer both practical utility and arguably greater interpretability. Veterinary pharmacology applications are generally well supported by relevant prior information, from either existing substantive knowledge, or an understanding of study and model design. This facilitates practical implementation of Bayesian analyses that can take advantage of this knowledge. This essay will explore the specification of Bayesian models relevant to veterinary pharmacology, including demonstration of prior selection, and illustrate the capability of these models to generate practically useful statistics, including uncertainty statements, that are difficult or impossible to obtain otherwise. Case studies using simulated data will describe applications in clinical trials, pharmacodynamics, and pharmacokinetics, all including multilevel modeling. This content may serve as a suitable starting point for researchers in veterinary pharmacology and related disciplines considering Bayesian estimation for their applied work.</p

The Surface Area to Volume Ratio Changes the Pharmacokinetic and Pharmacodynamic Parameters in the Subcutaneous Tissue Cage Model:As Illustrated by Carprofen in Sheep

Introduction: Pharmacokinetic and pharmacodynamic models can be powerful tools for predicting outcomes. Many models are based on repetitive sampling of the vascular space, due to the simplicity of obtaining samples. As many drugs do not exert their effect in the vasculature, models have been developed to sample tissues outside the bloodstream. Tissue cages are hollow devices implanted subcutaneously, or elsewhere, that are filled with fluid allowing repetitive sampling to occur. The physical dimensions of the cage, namely, the diffusible surface area to volume ratio, would be expected to change the rate of drug movement into and out of tissue cages. Methods: Seven sheep were implanted with five pairs of tissue cages, subcutaneously. Each pair of cages had a different length but a fixed diffusible surface area, so the surface area to volume ratio differed. Carrageenan was injected into half of the cages in each animal during one sampling period in a cross-over design. Samples from each cage and the bloodstream were obtained at 14-time points during two sampling periods. The concentration of carprofen was measured using LC–MS/MS and the results were modeled using nonlinear mixed-effects techniques. Prostaglandin metabolites were also measured and the change over time was analyzed using linear mixed effect modeling. Results: The presence of carrageenan within an animal changed the systemic pharmacokinetics of carprofen. The rate of drug movement into and out of the tissue cages varied with the surface area to volume ratio. The concentration time curve for prostaglandin metabolites changed with cage size. Conclusion: The surface area volume ratio of tissue cages will influence the calculated pharmacokinetic parameters and may affect calculated pharmacodynamics, thus, it is an important factor to consider when using tissue cage data for dosing regimes

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic

The aim of this longitudinal microbiome study was to investigate the effects of a commercially available veterinary synbiotic product (Blackmore's® Paw DigestiCare 60™) on the fecal microbiome of healthy dogs using 16S rRNA gene microbial profiling. Fifteen healthy, privately-owned dogs participated in a 2-week trial administration of the product. Fecal samples were collected at different time points, including baseline (prior to treatment), during administration and after discontinuation of product. Large intra- and inter-individual variation was observed throughout the study, but microbiome composition at higher phylogenetic levels, alpha and beta diversity were not significantly altered after 2 weeks of probiotic administration, suggesting an absence of probiotic impact on microbial diversity. Administration of the synbiotic preparation did, however, result in transient increases in probiotic species from Enterococacceae and Streptococacceae families as well as an increase in Fusobacteria; with the fecal microbiota partially reverting to its baseline state 3-weeks after cessation of probiotic administration

Pan-chromatic observations of the remarkable nova LMC 2012

We present the results of an intensive multiwavelength campaign on nova LMC 2012. This nova evolved very rapidly in all observed wavelengths. The time to fall two magnitudes in the V band was only 2 days. In X-rays the super soft phase began 13$\pm$5 days after discovery and ended around day 50 after discovery. During the super soft phase, the \Swift/XRT and \Chandra\ spectra were consistent with the underlying white dwarf being very hot, $\sim$ 1 MK, and luminous, $\sim$ 10$^{38}$ erg s$^{-1}$. The UV, optical, and near-IR photometry showed a periodic variation after the initial and rapid fading had ended. Timing analysis revealed a consistent 19.24$\pm$0.03 hr period in all UV, optical, and near-IR bands with amplitudes of $\sim$ 0.3 magnitudes which we associate with the orbital period of the central binary. No periods were detected in the corresponding X-ray data sets. A moderately high inclination system, $i$ = 60$\pm$10^{\arcdeg}, was inferred from the early optical emission lines. The {\it HST}/STIS UV spectra were highly unusual with only the \ion{N}{5} (1240\AA) line present and superposed on a blue continuum. The lack of emission lines and the observed UV and optical continua from four epochs can be fit with a low mass ejection event, $\sim$ 10$^{-6}$ M$_{\odot}$, from a hot and massive white dwarf near the Chandrasekhar limit. The white dwarf, in turn, significantly illuminated its subgiant companion which provided the bulk of the observed UV/optical continuum emission at the later dates. The inferred extreme white dwarf characteristics and low mass ejection event favor nova LMC 2012 being a recurrent nova of the U Sco subclass.Comment: 18 figures, 6 tables (one online only containing all the photometry

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic

The aim of this longitudinal microbiome study was to investigate the effects of a commercially available veterinary synbiotic product (Blackmore's® Paw DigestiCare 60™) on the fecal microbiome of healthy dogs using 16S rRNA gene microbial profiling. Fifteen healthy, privately-owned dogs participated in a 2-week trial administration of the product. Fecal samples were collected at different time points, including baseline (prior to treatment), during administration and after discontinuation of product. Large intra- and inter-individual variation was observed throughout the study, but microbiome composition at higher phylogenetic levels, alpha and beta diversity were not significantly altered after 2 weeks of probiotic administration, suggesting an absence of probiotic impact on microbial diversity. Administration of the synbiotic preparation did, however, result in transient increases in probiotic species from Enterococacceae and Streptococacceae families as well as an increase in Fusobacteria; with the fecal microbiota partially reverting to its baseline state 3-weeks after cessation of probiotic administration

Uncontrolled pain:a call for better study design

Studies assessing animal pain in veterinary research are often performed primarily for the benefit of animals. Frequently, the goal of these studies is to determine whether the analgesic effect of a novel treatment is clinically meaningful, and therefore has the capacity to improve the welfare of treated animals. To determine the treatment effect of a potential analgesic, control groups are necessary to allow comparison. There are negative control groups (where pain is unattenuated) and positive control groups (where pain is attenuated). Arising out of animal welfare concerns, there is growing reluctance to use negative control groups in pain studies. But for studies where pain is experimentally induced, the absence of a negative control group removes the opportunity to demonstrate that the study methods could differentiate a positive control intervention from doing nothing at all. For studies that are controlled by a single comparison group, the capacity to distinguish treatment effects from experimental noise is more difficult; especially considering that pain studies often involve small sample sizes, small and variable treatment effects, systematic error and use pain assessment measures that are unreliable. Due to these limitations, and with a focus on farm animals, we argue that many pain studies would be enhanced by the simultaneous inclusion of positive and negative control groups. This would help provide study-specific definitions of pain and pain attenuation, thereby permitting more reliable estimates of treatment effects. Adoption of our suggested refinements could improve animal welfare outcomes for millions of animals globally.</p

A Model of Fluid-Structure and Biochemical Interactions for Applications to Subclinical Leaflet Thrombosis

Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient ischemic attacks and strokes and can progress to clinical leaflet thrombosis. SLT following aortic valve replacement also may be related to subsequent structural valve deterioration, which can impair the durability of the valve replacement. Because of the difficulty in clinical imaging of SLT, models are needed to determine the mechanisms of SLT and could eventually predict which patients will develop SLT. To this end, we develop methods to simulate leaflet thrombosis that combine fluid-structure interaction and a simplified thrombosis model that allows for deposition along the moving leaflets. Additionally, this model can be adapted to model deposition or absorption along other moving boundaries. We present convergence results and quantify the model's ability to realize changes in valve opening and pressures. These new approaches are an important advancement in our tools for modeling thrombosis in which they incorporate both adhesion to the surface of the moving leaflets and feedback to the fluid-structure interaction.Comment: 29 pages, 11 figure

Deep-water incised valley deposits at the ediacaran-cambrian boundary in southern Namibia contain abundant treptichnus pedum

Valley-filling deposits of the Nama Group, southern Namibia, record two episodes of erosional downcutting and backfill, developed close together in time near the Ediacaran-Cambrian boundary. Geochronological constraints indicate that the older valley fill began 539.4 ± 1 Ma or later; the younger of these deposits contains unusually well-preserved populations of the basal Cambrian trace fossil Treptichnus pedum. Facies analysis shows that T. pedum is closely linked to a nearshore sandstone deposit, indicating a close environmental or taphonomic connection to very shallow, mud-draped sandy seafloor swept by tidal currents. Facies restriction may limit the biostratigraphic potential of T. pedum in Namibia and elsewhere, but it also illuminates functional and ecological interpretation. The T. pedum tracemaker was a motile bilaterian animal that lived below the sediment-water interface—propelling itself forward in upward-curving projections that breached the sediment surface. The T. pedum animal, therefore, lived infaunally, perhaps to avoid predation, surfacing regularly to feed and take in oxygen. Alternatively, the T. pedum animal may have been a deposit feeder that surfaced largely for purposes of gas exchange, an interpretation that has some support in the observed association of T. pedum with mud drapes. Treptichnus pedum provides our oldest record of animals that combined anatomical and behavioral complexity. Insights from comparative biology suggest that basal Cambrian T. pedum animals already possessed the anatomical, neurological, and genetic complexity needed to enable the body plan and behavioral diversification recorded by younger Cambrian fossils

Taphonomy of Biosignatures in Microbial Mats on Little Ambergris Cay, Turks and Caicos Islands

Microbial mats are taxonomically and metabolically diverse microbial ecosystems, with a characteristic layering that reflects vertical gradients in light and oxygen availability. Silicified microbial mats in Proterozoic carbonate successions are generally interpreted in terms of the surficial, mat building community. However, information about biodiversity in the once-surface-layer can be lost through decay as the mats accrete. To better understand how information about surface microbial communities is impacted by processes of decay within the mat, we studied microbial mats from Little Ambergris Cay, Turks and Caicos Islands. We used molecular techniques, microscopy and geochemistry to investigate microbial mat taphonomy – how processes of degradation affect biological signatures in sedimentary rocks, including fossils, molecular fossils and isotopic records. The top < 1 cm of these mats host cyanobacteria-rich communities overlying and admixed with diverse bacterial and eukaryotic taxa. Lower layers contain abundant, often empty, sheaths of large filamentous cyanobacteria, preserving their record as key mat-builders. Morphological remains and free lipid biomarkers of several bacterial groups, as well as diatoms, arthropods, and other eukaryotes also persist in lower mat layers, although at lower abundances than in surface layers. Carbon isotope signatures of organic matter were consistent with the majority of the biomass being sourced from CO2-limited cyanobacteria. Porewater sulfide sulfur isotope values were lower than seawater sulfate sulfur isotope values by ∼45–50‰, consistent with microbial sulfate reduction under sulfate-replete conditions. Our findings provide insight into how processes of degradation and decay bias biosignatures in the geological record of microbial mats, especially mats that formed widely during the Proterozoic (2,500–541 million years ago) Eon. Cyanobacteria were the key mat-builders, their robust and cohesive fabric retained at depth. Additionally, eukaryotic remains and eukaryotic biosignatures were preserved at depth, which suggests that microbial mats are not inherently biased against eukaryote preservation, either today or in the past

Five Years of Experimental Warming Increases the Biodiversity and Productivity of Phytoplankton

Phytoplankton are key components of aquatic ecosystems, fixing CO2 from the atmosphere through photosynthesis and supporting secondary production, yet relatively little is known about how future global warming might alter their biodiversity and associated ecosystem functioning. Here, we explore how the structure, function, and biodiversity of a planktonic metacommunity was altered after five years of experimental warming. Our outdoor mesocosm experiment was open to natural dispersal from the regional species pool, allowing us to explore the effects of experimental warming in the context of metacommunity dynamics. Warming of 4°C led to a 67% increase in the species richness of the phytoplankton, more evenly-distributed abundance, and higher rates of gross primary productivity. Warming elevated productivity indirectly, by increasing the biodiversity and biomass of the local phytoplankton communities. Warming also systematically shifted the taxonomic and functional trait composition of the phytoplankton, favoring large, colonial, inedible phytoplankton taxa, suggesting stronger top-down control, mediated by zooplankton grazing played an important role. Overall, our findings suggest that temperature can modulate species coexistence, and through such mechanisms, global warming could, in some cases, increase the species richness and productivity of phytoplankton communities