Scaled von Mises-Fisher distributions and regression models for paleomagnetic directional data

We propose a new distribution for analysing paleomagnetic directional data that is a novel transformation of the von Mises-Fisher distribution. The new distribution has ellipse-like symmetry, as does the Kent distribution; however, unlike the Kent distribution the normalising constant in the new density is easy to compute and estimation of the shape parameters is straightforward. To accommodate outliers, the model also incorporates an additional shape parameter which controls the tail-weight of the distribution. We also develop a general regression model framework that allows both the mean direction and the shape parameters of the error distribution to depend on covariates. The proposed regression procedure is shown to be equivariant with respect to the choice of coordinate system for the directional response. To illustrate, we analyse paleomagnetic directional data from the GEOMAGIA50.v3 database (Brown et al. 2015). We predict the mean direction at various geological 1 time points and show that there is significant heteroscedasticity present. It is envisaged that the regression structures and error distribution proposed here will also prove useful when covariate information is available with (i) other types of directional response data; and (ii) square-root transformed compositional data of general dimension

Characterizing Undetected Stellar Companions with Combined Datasets

Binaries play a critical role in the formation, evolution, and fundamental properties of planets, stars, and stellar associations. Observational studies in these areas often include a mix of observations aimed at detecting or ruling out the presence of stellar companions. Rarely can non-detections rule out all possible binary configurations. Here we present MOLUSC, our framework for constraining the range of properties of unseen companions using astrometric, imaging, and velocity information. We showcase the use of MOLUSC on a number of systems, ruling out stellar false positives in the signals of HIP67522b, and DS Tuc Ab. We also demonstrate how MOLUSC could be used to predict the number of missing companions in a stellar sample using the ZEIT sample of young planet hosts. Although our results are not significant, with a larger sample MOLUSC could be used to see if close-in planets are less common in young binary systems, as is seen for their older counterparts.Comment: 19 pages, 10 figures, 4 tables, Accepted to A

Assessment of Turbulent CFD Against STS-128 Hypersonic Flight Data

Turbulent CFD simulations are compared against surface temperature measurements of the space shuttle orbiter windward tiles at reentry flight conditions. Algebraic turbulence models are used within both the LAURA and DPLR CFD codes. The flight data are from temperature measurements obtained by seven thermocouples during the STS-128 mission (September 2009). The flight data indicate boundary layer transition onset over the Mach number range 13.5{15.5, depending upon the location on the vehicle. But the boundary layer flow appeared to be transitional down through Mach 12, based upon the flight data and CFD trends. At Mach 9 the simulations match the flight data on average within 20 F/11 C, where typical surface temperatures were approximately 1600 F/870 C

Anthocyanins inhibit tumor necrosis alpha-induced loss of Caco-2 cell barrier integrity

An increased permeability of the intestinal barrier is proposed as a major event in the pathophysiology of conditions characterized by chronic gut inflammation. This study investigated the capacity of pure anthocyanins (AC), and berry and rice extracts containing different types and amounts of AC, to inhibit tumor necrosis alpha (TNFα)-induced permeabilization of Caco-2 cell monolayers. Caco-2 cells differentiated into intestinal epithelial cell monolayers were incubated in the absence/presence of TNFα, with or without the addition of AC or AC-rich plant extracts (ACRE). AC and ACRE inhibited TNFα-induced loss of monolayer permeability as assessed by changes in transepithelial electrical resistance (TEER) and paracellular transport of FITC-dextran. In the range of concentrations tested (0.25–1 μM), O-glucosides of cyanidin, and delphinidin, but not those of malvidin, peonidin and petunidin protected the monolayer from TNFα-induced decrease of TEER and increase of FITC-dextran permeability. Cyanidin and delphinidin acted by mitigating TNFα-triggered activation of transcription factor NF-κB, and downstream phosphorylation of myosin light chain (MLC). The protective actions of the ACRE on TNFα-induced TEER increase was positively correlated with the sum of cyanidins and delphinidins (r2 = 0.83) content in the ACRE. However, no correlation was observed between TEER and ACRE total AC, malvidin, or peonidin content. Results support a particular capacity of cyanidins and delphinidins in the protection of the intestinal barrier against inflammation-induced permeabilization, in part through the inhibition of the NF-κB pathway.Fil: Cremonini, Eleonora. University of California at Davis; Estados UnidosFil: Mastaloudis, Angela. Nu Skin Enterprises; Estados UnidosFil: Hester, Shelly N.. Nu Skin Enterprises; Estados UnidosFil: Verstraeten, Sandra Viviana. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Anderson, Maureen. University of California at Davis; Estados UnidosFil: Wood, Steven M.. Nu Skin Enterprises; Estados UnidosFil: Waterhouse, Andrew L.. University of California at Davis; Estados UnidosFil: Fraga, César Guillermo. University of California at Davis; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Bioquímica y Medicina Molecular. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Bioquímica y Medicina Molecular; ArgentinaFil: Oteiza, Patricia Isabel. University of California at Davis; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Chimpanzees demonstrate individual differences in social information use

Studies of transmission biases in social learning have greatly informed our understanding of how behaviour patterns may diffuse through animal populations, yet within-species inter-individual variation in social information use has received little attention and remains poorly understood. We have addressed this question by examining individual performances across multiple experiments with the same population of primates. We compiled a dataset spanning 16 social learning studies (26 experimental conditions) carried out at the same study site over a 12-year period, incorporating a total of 167 chimpanzees. We applied a binary scoring system to code each participant’s performance in each study according to whether they demonstrated evidence of using social information from conspecifics to solve the experimental task or not (Social Information Score—‘SIS’). Bayesian binomial mixed effects models were then used to estimate the extent to which individual differences influenced SIS, together with any effects of sex, rearing history, age, prior involvement in research and task type on SIS. An estimate of repeatability found that approximately half of the variance in SIS was accounted for by individual identity, indicating that individual differences play a critical role in the social learning behaviour of chimpanzees. According to the model that best fit the data, females were, depending on their rearing history, 15–24% more likely to use social information to solve experimental tasks than males. However, there was no strong evidence of an effect of age or research experience, and pedigree records indicated that SIS was not a strongly heritable trait. Our study offers a novel, transferable method for the study of individual differences in social learning

Age-dependent patterns of bovine tuberculosis in cattle.

Bovine tuberculosis (BTB) is an important livestock disease, seriously impacting cattle industries in both industrialised and pre-industrialised countries. Like TB in other mammals, infection is life long and, if undiagnosed, may progress to disease years after exposure. The risk of disease in humans is highly age-dependent, however in cattle, age-dependent risks have yet to be quantified, largely due to insufficient data and limited diagnostics. Here, we estimate age-specific reactor rates in Great Britain by combining herd-level testing data with spatial movement data from the Cattle Tracing System (CTS). Using a catalytic model, we find strong age dependencies in infection risk and that the probability of detecting infection increases with age. Between 2004 and 2009, infection incidence in cattle fluctuated around 1%. Age-specific incidence increased monotonically until 24-36 months, with cattle aged between 12 and 36 months experiencing the highest rates of infection. Beef and dairy cattle under 24 months experienced similar infection risks, however major differences occurred in older ages. The average reproductive number in cattle was greater than 1 for the years 2004-2009. These methods reveal a consistent pattern of BTB rates with age, across different population structures and testing patterns. The results provide practical insights into BTB epidemiology and control, suggesting that targeting a mass control programme at cattle between 12 and 36 months could be beneficial.EBP is funded by an Engineering and Physical Sciences Research Council (EPSRC) fellowship. JLNW is supported by the Alborada Trust and the RAPIDD program of the Science & Technology Directorate, U.S. Department of Homeland Security, and the Fogarty International Center, U.S. National Institutes of Health. AJKC is supported by Defra grant no. SE-3127. TJM is supported by the BBSRC. We thank Steve Holdship and Rose Nicholson at Defra the AHVLA team for providing access to the CTS and VetNet

A metagenomic assessment of the bacteria associated with Lucilia sericata and Lucilia cuprina (Diptera: Calliphoridae)

Lucilia Robineau-Desvoidy (Diptera: Calliphoridae) is a blow fly genus of forensic, medical, veterinary, and agricultural importance. This genus is also famous because of its beneficial uses in maggot debridement therapy (MDT). Although the genus is of considerable economic importance, our knowledge about microbes associated with these flies and how these bacteria are horizontally and trans-generationally transmitted is limited. In this study, we characterized bacteria associated with different life stages of Lucilia sericata (Meigen) and Lucilia cuprina(Wiedemann) and in the salivary gland of L. sericata by using 16S rDNA 454 pyrosequencing. Bacteria associated with the salivary gland of L. sericata were also characterized using light and transmission electron microscopy (TEM). Results from this study suggest that the majority of bacteria associated with these flies belong to phyla Proteobacteria, Firmicutes, andBacteroidetes, and most bacteria are maintained intragenerationally, with a considerable degree of turnover from generation to generation. In both species, second-generation eggs exhibited the highest bacterial phylum diversity (20 % genetic distance) than other life stages. The Lucilia sister species shared the majority of their classified genera. Of the shared bacterial genera, Providencia, Ignatzschineria, Lactobacillus, Lactococcus, Vagococcus, Morganella, and Myroides were present at relatively high abundances. Lactobacillus, Proteus,Diaphorobacter, and Morganella were the dominant bacterial genera associated with a survey of the salivary gland of L. sericata. TEM analysis showed a sparse distribution of both Gram-positive and Gram-negative bacteria in the salivary gland of L. sericata. There was more evidence for horizontal transmission of bacteria than there was for trans-generational inheritance. Several pathogenic genera were either amplified or reduced by the larval feeding on decomposing liver as a resource. Overall, this study provides information on bacterial communities associated with different life stages of Lucilia and their horizontal and trans-generational transmission, which may help in the development of better vector-borne disease management and MDT methods

Comparability of macroinvertebrate biomonitoring indices of river health derived from semi-quantitative and quantitative methodologies

Aquatic macroinvertebrates have been the basis for one of the primary indicators and a cornerstone of lotic biomonitoring for over 40 years. Despite the widespread use of lotic invertebrates in statutory biomonitoring networks, scientific research and citizen science projects, the sampling methodologies employed frequently vary between studies. Routine statutory biomonitoring has historically relied on semi-quantitative sampling methods (timed kick sampling), while much academic research has favoured fully quantitative methods (e.g. Surber sampling). There is an untested assumption that data derived using quantitative and semi-quantitative samples are not comparable for biomonitoring purposes. As a result, data derived from the same site, but using different sampling techniques, have typically not been analysed together or directly compared. Here, we test this assumption by comparing a range of biomonitoring metrics derived from data collected using timed semi-quantitative kick samples and quantitative Surber samples from the same sites simultaneously. In total, 39 pairs of samples from 7 rivers in the UK were compared for two seasons (spring and autumn). We found a strong positive correlation (rs = +0.84) between estimates of taxa richness based on ten Surber sub-samples and a single kick sample. The majority of biomonitoring metrics were comparable between techniques, although only fully quantitative sampling allows the density of the community (individual m−2) to be determined. However, this advantage needs to be balanced alongside the greater total sampling time and effort associated with the fully quantitative methodology used here. Kick samples did not provide a good estimate of relative abundance of a number of species/taxa and, therefore, the quantitative method has the potential to provide important additional information which may support the interpretation of the biological metrics